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Team:Freiburg software/Code/BioBrickManager.java
From 2009.igem.org
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Latest revision as of 00:11, 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;}
}
