/* $RCSfile$
* $Author$
* $Date$
* $Revision$
*
* 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>
*/
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
*/
public String getStrandName() {
return strandName;
}
/**
* Retrieves the strand type.
*
* @return The type of the Strand object
* @see #setStrandType
*/
public String getStrandType() {
return strandType;
}
/**
* Sets the name of the Strand object.
*
* @param cStrandName The new name for this strand
* @see #getStrandName
*/
public void setStrandName(String cStrandName) {
strandName = cStrandName;
}
/**
* Sets the type of the Strand object.
*
* @param cStrandType The new type for this strand
* @see #getStrandType
*/
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
*
*/
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
*
*/
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
*
*/
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
*
*/
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.
*/
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
*/
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.
*/
public Map<String, IMonomer> getMonomers() {
return monomers;
}
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();
}
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;
}
}