/* $RCSfile$
* $Author$
* $Date$
* $Revision$
*
* Copyright (C) 2005-2007 Miguel Rojas <miguelrojas@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.
*
* 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.tools.periodictable;
import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.tools.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.util.List;
/**
* Used to store and return data of a particular chemicalElement. As this class is a
* singleton class, one gets an instance with:
* <pre>
* ElementPTFactory efac = ElementPTFactory.getInstance();
* </pre>
*
* @author Miguel Rojas
* @cdk.created May 8, 2005
* @cdk.module standard
* @cdk.githash
*/
@TestClass("org.openscience.cdk.tools.periodictable.ElementPTFactoryTest")
class ElementPTFactory
{
private static ElementPTFactory efac = null;
private List<PeriodicTableElement> elements = null;
private boolean debug = false;
private static ILoggingTool logger =
LoggingToolFactory.createLoggingTool(ElementPTFactory.class);
/**
* Private constructor for the ElementPTFactory object.
*
*@exception IOException A problem with reading the chemicalElements.xml file
*/
private ElementPTFactory() throws IOException
{
logger.info("Creating new ElementPTFactory");
InputStream ins = null;
String errorMessage = "There was a problem getting org.openscience.cdk." +
"config.chemicalElements.xml as a stream";
try {
String configFile = "org/openscience/cdk/config/data/chemicalElements.xml";
if (debug) logger.debug("Getting stream for ", configFile);
ins = this.getClass().getClassLoader().getResourceAsStream(configFile);
} catch (Exception exception) {
logger.error(errorMessage);
logger.debug(exception);
throw new IOException(errorMessage);
}
if (ins == null) {
logger.error(errorMessage);
throw new IOException(errorMessage);
}
ElementPTReader reader = new ElementPTReader(new InputStreamReader(ins));
elements = reader.readElements();
if (debug) logger.debug("Found #elements in file: ", elements.size());
}
/**
* Returns an ElementPTFactory instance.
*
*@return The instance value
*@exception IOException Description of the Exception
*/
@TestMethod("testGetInstance")
public static ElementPTFactory getInstance() throws IOException
{
if (efac == null)
{
efac = new ElementPTFactory();
}
return efac;
}
/**
* Returns the number of elements defined by this class.
*
*@return The size value
*/
@TestMethod("testGetSize")
public int getSize()
{
return elements.size();
}
/**
* Get all the elements loaded by the factory.
*
* @return A Vector of PeriodicTableElement objects
* @see org.openscience.cdk.tools.periodictable.PeriodicTableElement
*/
@TestMethod("testGetElements")
public List<PeriodicTableElement> getElements() {
return elements;
}
/**
* Returns an Element with a given element symbol.
*
*@param symbol An element symbol to search for
*@return An array of element that matches the given element symbol
*/
@TestMethod("testGetElement_String")
public PeriodicTableElement getElement(String symbol) {
for (PeriodicTableElement element : elements) {
if (element.getSymbol().equals(symbol)) {
try {
return (PeriodicTableElement) element.clone();
} catch (CloneNotSupportedException e) {
logger.error("Could not clone PeriodicTableElement: ", e.getMessage());
logger.debug(e);
}
}
}
return null;
}
/**
* Configures a PeriodicTableElement. Finds the correct element type
* by looking at the element symbol.
*
*@param element The PeriodicTableElement to be configure
*@return The configured PeriodicTableElement
* @throws org.openscience.cdk.exception.CDKException if there is an error during configuration
* (such as invalid IUPAC group number)
*/
@TestMethod("testConfigure_PeriodicTableElement")
public PeriodicTableElement configure(PeriodicTableElement element) throws CDKException {
PeriodicTableElement elementInt = getElement(element.getSymbol());
element.setSymbol(elementInt.getSymbol());
element.setAtomicNumber(elementInt.getAtomicNumber());
element.setName(elementInt.getName());
element.setChemicalSerie(elementInt.getChemicalSerie());
element.setPeriod(elementInt.getPeriod());
if(elementInt.getGroup()!=null)
element.setGroup(elementInt.getGroup());
element.setPhase(elementInt.getPhase());
element.setCASid(elementInt.getCASid());
element.setPaulingEneg(elementInt.getPaulingEneg());
return element;
}
/**
* Gets the atomic number of this element in the periodic table.
*
* @param element The PeriodicTableElement object
* @return The atomic number value
*/
@TestMethod("testGetAtomicNumber_PeriodicTableElement")
public double getAtomicNumber(PeriodicTableElement element){
PeriodicTableElement elementInt = getElement(element.getSymbol());
return elementInt.getAtomicNumber();
}
/**
* Gets the name of this element in the periodic table.
*
* @param element The PeriodicTableElement object
* @return The name value of this element
*/
@TestMethod("testGetName_PeriodicTableElement")
public String getName(PeriodicTableElement element){
PeriodicTableElement elementInt = getElement(element.getSymbol());
return elementInt.getName();
}
/**
* Gets the chemical serie of this element in the periodic table.
*
* @param element The PeriodicTableElement object
* @return The chemical serie value of this element
*/
@TestMethod("testGetChemicalSerie_PeriodicTableElement")
public String getChemicalSerie(PeriodicTableElement element){
PeriodicTableElement elementInt = getElement(element.getSymbol());
return elementInt.getChemicalSerie();
}
/**
* Gets the period of this element in the periodic table.
*
* @param element The PeriodicTableElement object
* @return The period value of this element
*/
@TestMethod("testGetPeriod_PeriodicTableElement")
public int getPeriod(PeriodicTableElement element){
org.openscience.cdk.tools.periodictable.PeriodicTableElement elementInt = getElement(element.getSymbol());
return elementInt.getPeriod();
}
/**
* Gets the group of this element in the periodic table.
*
* @param element The PeriodicTableElement object
* @return The group value of this element
*/
@TestMethod("testGetGroup_PeriodicTableElement")
public int getGroup(PeriodicTableElement element){
PeriodicTableElement elementInt = getElement(element.getSymbol());
return elementInt.getGroup();
}
/**
* Gets the phase of this element in the periodic table.
*
* @param element The PeriodicTableElement object
* @return The phase value of this element
*/
@TestMethod("testGetPhase_PeriodicTableElement")
public String getPhase(PeriodicTableElement element){
PeriodicTableElement elementInt = getElement(element.getSymbol());
return elementInt.getPhase();
}
/**
* Gets the CAS id of this element in the periodic table.
*
* @param element The PeriodicTableElement object
* @return The CASE id value of this element
*/
@TestMethod("testGetCASid_PeriodicTableElement")
public String getCASid(PeriodicTableElement element){
org.openscience.cdk.tools.periodictable.PeriodicTableElement elementInt = getElement(element.getSymbol());
return elementInt.getCASid();
}
/**
* Gets the Vdw radios of this element in the periodic table.
*
* @param element The PeriodicTableElement object
* @return The Vdw radio value of this element
*/
@TestMethod("testGetVdwRadius_PeriodicTableElement")
public double getVdwRadius(PeriodicTableElement element){
PeriodicTableElement elementInt = getElement(element.getSymbol());
return elementInt.getVdwRadius();
}
/**
* Gets the covalent radios of this element in the periodic table.
*
* @param element The PeriodicTableElement object
* @return The covalent radio value of this element
*/
@TestMethod("testGetCovalentRadius_PeriodicTableElement")
public double getCovalentRadius(PeriodicTableElement element){
PeriodicTableElement elementInt = getElement(element.getSymbol());
return elementInt.getCovalentRadius();
}
/**
* Gets the Pauling Electronegativity radios of this element in the periodic table.
*
* @param element The PeriodicTableElement object
* @return The Pauling Electronegativity value of this element
*/
@TestMethod("testGetPaulingEneg_PeriodicTableElement")
public double getPaulingEneg(PeriodicTableElement element){
PeriodicTableElement elementInt = getElement(element.getSymbol());
return elementInt.getPaulingEneg();
}
}