/* * BioJava development code * * This code may be freely distributed and modified under the * terms of the GNU Lesser General Public Licence. This should * be distributed with the code. If you do not have a copy, * see: * * http://www.gnu.org/copyleft/lesser.html * * Copyright for this code is held jointly by the individual * authors. These should be listed in @author doc comments. * * For more information on the BioJava project and its aims, * or to join the biojava-l mailing list, visit the home page * at: * * http://www.biojava.org/ */ package org.biojava.bio.dist; import java.io.IOException; import java.io.InputStream; import java.io.InputStreamReader; import java.util.ArrayList; import java.util.List; import javax.xml.parsers.ParserConfigurationException; import javax.xml.parsers.SAXParser; import javax.xml.parsers.SAXParserFactory; import org.biojava.bio.BioException; import org.biojava.bio.seq.io.SymbolTokenization; import org.biojava.bio.symbol.Alphabet; import org.biojava.bio.symbol.AlphabetManager; import org.biojava.bio.symbol.AtomicSymbol; import org.biojava.bio.symbol.IllegalAlphabetException; import org.biojava.bio.symbol.IllegalSymbolException; import org.biojava.bio.symbol.Symbol; import org.biojava.utils.ChangeVetoException; import org.xml.sax.Attributes; import org.xml.sax.InputSource; import org.xml.sax.SAXException; import org.xml.sax.helpers.DefaultHandler; /** * A SAX parser that reads an XML representation of a * Distribution from a file and recreates it as a Distribution Object. * Handles OrderNDistributions and Simple Distributions but * ensure the OrderNDistributions being read in was made using * conditioning and conditioned Alphabets. * * @author Russell Smithies * @author Mark Schreiber * @author Matthew Pocock * @since 1.3 */ public class XMLDistributionReader extends DefaultHandler { //fixme: the handler and the user API seem to be muddled up - can the // DefaultHandler impl be factored out into a static and hopefully private // class? private Alphabet alpha = null; private Distribution dist = null; private DistributionFactory fact = null; //private OrderNDistributionFactory ondFact = null; private SymbolTokenization nameParser = null; private Symbol sym = null; private Alphabet conditioningAlpha = null; private AtomicSymbol conditioningSymbol = null; private SymbolTokenization conditioningTok = null; private Alphabet conditionedAlpha = null; private AtomicSymbol conditionedSymbol = null; private SymbolTokenization conditionedTok = null; private Distribution getDist() { return dist; } //end getDist /** * Reads an XML representation of a Distribution from a file. * * @param is input in XML format * @return dist the Distribution created. * @throws IOException if an error occurs during reading. * @throws SAXException if the XML is not as expected. */ public Distribution parseXML(InputStream is) throws IOException, SAXException{ //org.xml.sax.XMLReader parser = new org.apache.xerces.parsers.SAXParser(); SAXParserFactory fact = SAXParserFactory.newInstance(); fact.setNamespaceAware(true); try { SAXParser parser = fact.newSAXParser(); // parser.setContentHandler(this); // // parser.setErrorHandler(this); InputSource xml = null; xml = new InputSource(new InputStreamReader(is)); parser.parse(xml, this); } catch (ParserConfigurationException ex) { //really shouldn't happen throw new SAXException("Cannot make SAXParser",ex); } return this.getDist(); } /** * Required by SAXParser to be public. * *
* It is not reccomended that you use this method directly. Use ParseXML * instead. *
*/ public void startElement(String nameSpaceURI, String localName, String rawName, Attributes attributes) throws SAXException{ if (localName.equals("Distribution") || localName.equals("OrderNDistribution")) { processDistElement(attributes); } else if (localName.equals("alphabet")) { processAlphabetElement(attributes); } else if (localName.equals("conditioning_symbol")) { processConditioningSymbol(attributes); } else if (localName.equals("weight")) { processWeightElement(attributes); } } //end startElement private void processConditioningSymbol(Attributes attr) throws SAXException { String name = attr.getValue("name"); try { conditioningSymbol = (AtomicSymbol)conditioningTok.parseToken(name); } catch (IllegalSymbolException ex) { throw new SAXException(ex); } } private void processWeightElement(Attributes attr) throws SAXException{ double weight = 0.0; try { //get the weight of the symbol weight = Double.parseDouble(attr.getValue("prob")); } catch (NumberFormatException ex) { //catches the "NAN" string weight = 0.0; } //add counts if SIMPLE DISTRIBUTION if ((dist instanceof OrderNDistribution) == false) { try { //initialize the tokenizer nameParser = dist.getAlphabet().getTokenization("name"); } catch (BioException ex) { throw new SAXException("Couldn't get tokenization for " +dist.getAlphabet().getName(), ex); } try { //get the symbol name sym = nameParser.parseToken(attr.getValue("sym")); //add count to dist dist.setWeight(sym, weight); } catch (IllegalSymbolException ex) { throw new SAXException("Illegal symbol found", ex); } catch (ChangeVetoException ex) { throw new SAXException("Distribution has been locked, possible synchronization problem !?",ex); } //add countf if ORDER N DISTRIBUTION } else if (dist instanceof OrderNDistribution) { //get the weight for symbol try { //get the weight of the symbol weight = Double.parseDouble(attr.getValue("prob")); } catch (NumberFormatException ex) { weight = 0.0; } //rebuild the symbol from the conditioning and conditioned symbol String name = attr.getValue("sym"); try { conditionedSymbol = (AtomicSymbol)conditionedTok.parseToken(name); } catch (IllegalSymbolException ex) { throw new SAXException(ex); } List l = new ArrayList(); l.add(conditioningSymbol); l.add(conditionedSymbol); try { sym = alpha.getSymbol(l); //set weights on distribution dist.setWeight(sym, weight); } catch (IllegalSymbolException ex) { throw new SAXException("Illegal symbol found", ex); } catch (ChangeVetoException ex) { throw new SAXException("Distribution has been locked, possible synchronization problem !?",ex); } } } //end processWeight private void processAlphabetElement(Attributes attr) throws SAXException { String alphaName = attr.getValue("name"); //get Alphabet alpha = AlphabetManager.alphabetForName(alphaName); //make the Distribution try { dist = fact.createDistribution(alpha); if(dist instanceof OrderNDistribution){ conditionedAlpha = ((OrderNDistribution)dist).getConditionedAlphabet(); conditionedTok = conditionedAlpha.getTokenization("name"); conditioningAlpha = ((OrderNDistribution)dist).getConditioningAlphabet(); conditioningTok = conditioningAlpha.getTokenization("name"); } } catch (IllegalAlphabetException ex) { throw new SAXException(ex); } catch (BioException ex) { throw new SAXException(ex); } } //end processAlphabetElement private void processDistElement(Attributes attr) throws SAXException { if (attr.getValue("type").equals("Distribution")) { fact = DistributionFactory.DEFAULT; } else if (attr.getValue("type").equals("OrderNDistribution")) { fact = OrderNDistributionFactory.DEFAULT; } else { throw new SAXException("Element must be a distribution"); } } //end processDistElement }