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ElementPTHandler.java
/* $RCSfile$
 * $Author$
 * $Date$
 * $Revision$
 *
 * Copyright (C) 2003-2007  The Chemistry Development Kit (CDK) project
 *
 * Contact: cdk-devel@lists.sf.net
 *
 *  This library 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 library 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 library; if not, write to the Free Software
 *  Foundation, 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. 
 */
package org.openscience.cdk.config.elements;

import org.openscience.cdk.PeriodicTableElement;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.tools.LoggingTool;
import org.xml.sax.Attributes;
import org.xml.sax.helpers.DefaultHandler;

import java.util.ArrayList;
import java.util.List;

/**
 * Reads an element list in CML2 format. An example definition is:
 * <pre>
 * <elementType id="Li">
 *     <label dictRef="cas:id">7439-93-2</label>
 *     <scalar dataType="xsd:Integer" dictRef="cdk:group">1</scalar>
 *     <scalar dataType="xsd:Integer" dictRef="cdk:period">2</scalar>
 *     <scalar dataType="xsd:String" dictRef="cdk:name">Lithium</scalar>
 *     <scalar dataType="xsd:Integer" dictRef="cdk:atomicNumber">3</scalar>
 *     <scalar dataType="xsd:String" dictRef="cdk:chemicalSerie">Alkali Metals</scalar>
 *     <scalar dataType="xsd:String" dictRef="cdk:phase">Solid</scalar>
 * </elementType>
 * </pre> 
 *
 * @author           Miguel Rojas
 * @cdk.created    May 8, 2005
 * @cdk.module     extra
 * @cdk.githash
 */
00054 public class ElementPTHandler extends DefaultHandler 
{
      private final int SCALAR_UNSET = 0;
      private final int LABEL_CAS = 1; 
      private final int SCALAR_NAME = 2; 
      private final int SCALAR_ATOMICNUMBER = 3;
      private final int SCALAR_CHEMICALSERIE = 4;
      private final int SCALAR_PERIOD = 5;
      private final int SCALAR_GROUP = 6;
      private final int SCALAR_PHASE = 7;
      private final int SCALAR_RADCOV = 8;
      private final int SCALAR_RADVDW = 9;
      private final int SCALAR_PAULE = 10;
      private int scalarType;
      private LoggingTool logger;
      private String currentChars;
      private List<PeriodicTableElement> elements;
      
      public PeriodicTableElement elementType;
      public String currentElement;
      public String dictRef;
      
      public ElementPTHandler() 
      {
            logger = new LoggingTool(this);
      }

      /** 
      * Returns the element read from the XML file.
      *
      * @return A Vector object with all isotopes
      */
00086       public List<PeriodicTableElement> getElements() 
      {
            return elements;
      }

      // SAX Parser methods

      public void startDocument() 
      {
            elements = new ArrayList<PeriodicTableElement>();
            scalarType = SCALAR_UNSET;
            elementType = null;
      }

      public void endElement(String uri, String local, String raw) {
            logger.debug("end element: ", raw);
            if ("elementType".equals(local)) 
            {
                  elements.add(elementType);
            } else if ("label".equals(local)) {
                  currentChars.trim();
                  try {
                        if (scalarType == LABEL_CAS)
                              elementType.setCASid(currentChars);
                        } catch (NumberFormatException exception) {
                              logger.error("The abundance value is incorrect: ", currentChars);
                              logger.debug(exception);
                        }
                  
            }else if ("scalar".equals(local)) {
                  currentChars.trim();
                  try {
                        if (scalarType == SCALAR_NAME){
                              elementType.setName(currentChars);
                        } else if (scalarType == SCALAR_ATOMICNUMBER) {
                              elementType.setAtomicNumber(Integer.parseInt(currentChars));
                        } else if (scalarType == SCALAR_CHEMICALSERIE) {
                              elementType.setChemicalSerie(currentChars);
                        } else if (scalarType == SCALAR_PERIOD) {
                              elementType.setPeriod(Integer.parseInt(currentChars));
                        } else if (scalarType == SCALAR_GROUP) {
                        elementType.setGroup(Integer.parseInt(currentChars));
                } else if (scalarType == SCALAR_PHASE) {
                              elementType.setPhase(currentChars);
                        }else if (scalarType == SCALAR_RADCOV) {
                              elementType.setCovalentRadius(Double.parseDouble(currentChars));
                        }else if (scalarType == SCALAR_RADVDW) {
                              elementType.setVdwRadius(Double.parseDouble(currentChars));
                        } else if (scalarType == SCALAR_PAULE) {
                              elementType.setPaulingEneg(Double.parseDouble(currentChars));
                        }  
                  } catch (NumberFormatException exception) {
                        logger.error("The abundance value is incorrect: ", currentChars);
                        logger.debug(exception);
                  } catch (CDKException e) {
                logger.error("Invalid IUPAC group number is specified");
            }
            scalarType = SCALAR_UNSET;
            }
            currentChars = "";
      }

      public void startElement(String uri, String local, 
                             String raw, Attributes atts) 
      {
            currentChars = "";
            dictRef = "";
            logger.debug("startElement: ", raw);
            logger.debug("uri: ", uri);
            logger.debug("local: ", local);
            logger.debug("raw: ", raw);
            if ("elementType".equals(local)) {
                  for (int i = 0; i < atts.getLength(); i++) {
                        if ("id".equals(atts.getQName(i))) {
                              elementType = new PeriodicTableElement(atts.getValue(i));
                        }
                  }
            }else if ("label".equals(local)){
                  for (int i = 0; i < atts.getLength(); i++) {
                        if ("dictRef".equals(atts.getQName(i))) {
                              if ("cas:id".equals(atts.getValue(i))) {
                                    scalarType = LABEL_CAS;
                              }
                        }
                  }
            }else if ("scalar".equals(local)) 
                  for (int i = 0; i < atts.getLength(); i++) {
                        if ("dictRef".equals(atts.getQName(i))) {
                              if ("cdk:name".equals(atts.getValue(i))) {
                                    scalarType = SCALAR_NAME;
                              } else if ("cdk:atomicNumber".equals(atts.getValue(i))) {
                                    scalarType = SCALAR_ATOMICNUMBER;
                              } else if ("cdk:name".equals(atts.getValue(i))) {
                                    scalarType = SCALAR_NAME;
                              } else if ("cdk:chemicalSerie".equals(atts.getValue(i))) {
                                    scalarType = SCALAR_CHEMICALSERIE;
                              } else if ("cdk:period".equals(atts.getValue(i))) {
                                    scalarType = SCALAR_PERIOD;
                              } else if ("cdk:group".equals(atts.getValue(i))) {
                                    scalarType = SCALAR_GROUP;
                              } else if ("cdk:phase".equals(atts.getValue(i))) {
                                    scalarType = SCALAR_PHASE;
                              } else if ("cdk:radiiCova".equals(atts.getValue(i))) {
                                    scalarType = SCALAR_RADCOV;
                              } else if ("cdk:radiiVdw".equals(atts.getValue(i))) {
                                    scalarType = SCALAR_RADVDW;
                              } else if ("cdk:paulingE".equals(atts.getValue(i))) {
                                    scalarType = SCALAR_PAULE;
                              }
                              
                        }
                  }
                        
      }
      
      public void characters(char chars[], int start, int length) 
      {
            logger.debug("character data");
            currentChars += new String(chars, start, length);
      }

}

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