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From 2009.igem.org

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Revision as of 00:09, 22 October 2009

/* Copyright: synbiowave License: GPL Authors: Jörg Wassolesk Version: 0.1 DESCRIPTION: This class is used as main class for managing BioBrick DAS connections. */ package org.synbiowave.biobrick; import java.io.IOException; import java.io.InputStream; import java.net.HttpURLConnection; import java.net.URL; import java.util.List; import java.util.Map; import java.util.TreeSet; import java.util.zip.GZIPInputStream; import javax.xml.parsers.ParserConfigurationException; import javax.xml.parsers.SAXParser; import javax.xml.parsers.SAXParserFactory; import org.xml.sax.InputSource; import org.xml.sax.SAXException; import org.xml.sax.SAXNotRecognizedException; import org.xml.sax.XMLReader; // TODO: Auto-generated Javadoc /** * The Class BioBrickManager. */ public class BioBrickManager{ /** * Instantiates a new bio brick manager. */ public BioBrickManager(){} /** * Read bio brick features. * * @param id the id * * @return the list< map< string, string>> * * @throws IOException Signals that an I/O exception has occurred. * @throws SAXException the SAX exception */ public static List<Map<String,String>> readBioBrickFeatures(String id) throws IOException,SAXException{ String url="http://partsregistry.org/das/parts/features/?segment="+id; InputStream stream=getBioBrickStream(url); XMLReader xmlreader=getBioBrickReader(); BioBrick_DAS_Feature_Handler cont_handle=new BioBrick_DAS_Feature_Handler(); xmlreader.setContentHandler(cont_handle); xmlreader.setErrorHandler(new org.xml.sax.helpers.DefaultHandler()); InputSource insource=new InputSource(); insource.setByteStream(stream); xmlreader.parse(insource); return cont_handle.get_features();} /** * Read bio brick sequence. * * @param id the id * * @return the string * * @throws IOException Signals that an I/O exception has occurred. * @throws SAXException the SAX exception */ public static String readBioBrickSequence(String id) throws IOException,SAXException{ String url="http://partsregistry.org/das/parts/dna/?segment="+id; InputStream stream=getBioBrickStream(url); XMLReader xmlreader=getBioBrickReader(); BioBrick_DAS_DNA_Handler cont_handle=new BioBrick_DAS_DNA_Handler(); xmlreader.setContentHandler(cont_handle); xmlreader.setErrorHandler(new org.xml.sax.helpers.DefaultHandler()); InputSource insource=new InputSource(); insource.setByteStream(stream); xmlreader.parse(insource); return cont_handle.get_sequence();} /** * Read bio brick i ds. * * @return the tree set< string> * * @throws IOException Signals that an I/O exception has occurred. * @throws SAXException the SAX exception */ public static TreeSet<String> readBioBrickIDs() throws IOException,SAXException{ String url="http://partsregistry.org/das/parts/entry_points/"; InputStream stream=getBioBrickStream(url); XMLReader xmlreader=getBioBrickReader(); BioBrick_DAS_Entry_Points_Handler cont_handle=new BioBrick_DAS_Entry_Points_Handler(); xmlreader.setContentHandler(cont_handle); xmlreader.setErrorHandler(new org.xml.sax.helpers.DefaultHandler()); InputSource insource=new InputSource(); insource.setByteStream(stream); xmlreader.parse(insource); return cont_handle.getIDs();} /** * Gets the bio brick stream. * * @param urlPath the url path * * @return the bio brick stream * * @throws IOException Signals that an I/O exception has occurred. */ public static InputStream getBioBrickStream(String urlPath) throws IOException{ URL url=new URL(urlPath); HttpURLConnection huc=(HttpURLConnection)url.openConnection(); huc.setRequestProperty("Accept-Encoding","gzip"); String contentEncoding=huc.getContentEncoding(); InputStream stream=huc.getInputStream(); if(contentEncoding!=null){ if(contentEncoding.indexOf("gzip")!=-1){stream=new GZIPInputStream(stream);}} return stream;} /** * Gets the bio brick reader. * * @return the bio brick reader * * @throws SAXException the SAX exception */ private static XMLReader getBioBrickReader() throws SAXException{ SAXParserFactory spfactory=SAXParserFactory.newInstance(); spfactory.setValidating(false); SAXParser saxParser = null ; try{saxParser=spfactory.newSAXParser();} catch(ParserConfigurationException e){System.out.println(e.toString());} String vali=System.getProperty("XMLVALIDATION"); boolean validation=false ; if(vali!=null){if(vali.equals("true")){validation=true;}} XMLReader xmlreader=saxParser.getXMLReader(); try{xmlreader.setFeature("http://xml.org/sax/features/validation",validation);} catch(SAXException e){System.out.println(e.toString());} try{xmlreader.setFeature("http://apache.org/xml/features/nonvalidating/load-external-dtd",validation);} catch(SAXNotRecognizedException e){System.out.println(e.toString());} return xmlreader;} }

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