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Strand.java
/* $RCSfile$
 * $Author$
 * $Date$
 * $Revision$
 * 
 * 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;

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  data
 * @cdk.githash
 * @cdk.created 2004-12-20
 * @author      Martin Eklund <martin.eklund@farmbio.uu.se>
 * @author      Ola Spjuth <ola.spjuth@farmbio.uu.se>
 */
00049 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>.
       */
00059       private static final long serialVersionUID = 4200943086350928356L;

      /** The list of all Monomers in the Strand.*/
00062       private Map<String, IMonomer> monomers;
      /** The name of this strand (e.g. A, B). */
00064       private String strandName;
      /** The type of this strand (e.g. PEPTIDE, DNA, RNA). */
00066       private String strandType;
      
      /**
       * Constructs a new Strand.
       */   
00071       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
       */
00088       public String getStrandName() {
            return strandName;
      }
      
      /**
       * Retrieves the strand type.
       *
       * @return The type of the Strand object
       * @see #setStrandType
       */
00098       public String getStrandType() {
            return strandType;
      }
      
      /**
       * Sets the name of the Strand object.
       *
       * @param cStrandName  The new name for this strand
       * @see #getStrandName
       */
00108       public void setStrandName(String cStrandName) {
            strandName = cStrandName;
      }
      
      /**
       * Sets the type of the Strand object.
       *
       * @param cStrandType  The new type for this strand
       * @see #getStrandType
       */
00118       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
       *
       */
00130       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
       *
       */
00142       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
       *
       */
00169       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
       *
       */
00181       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.
       */
00191       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
       */
00214       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.
       */
00227       public Map<String, IMonomer> getMonomers()      {
            return monomers;
      }
    
00231     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();
    }
    
00246     public Object 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;
    }
}

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