*/
package org.biojava.dasobert.das2.io;
-import java.io.InputStream;
-import java.net.HttpURLConnection;
-import java.net.URL;
+import java.io.*;
+import java.net.*;
+import javax.xml.parsers.*;
+import org.biojava.dasobert.das.*;
+import org.biojava.dasobert.dasregistry.*;
+import org.xml.sax.*;
-import javax.xml.parsers.ParserConfigurationException;
-import javax.xml.parsers.SAXParser;
-import javax.xml.parsers.SAXParserFactory;
+public class DasSourceReaderImpl implements DasSourceReader
+{
-//import org.biojava.dasobert.das.AlignmentThread;
-import org.biojava.dasobert.das.DAS_FeatureRetrieve;
-import org.biojava.dasobert.dasregistry.DasSource;
-import org.xml.sax.InputSource;
-import org.xml.sax.SAXException;
-import org.xml.sax.SAXNotRecognizedException;
-import org.xml.sax.XMLReader;
+ Exception loggedException;
-public class DasSourceReaderImpl implements DasSourceReader {
+ public DasSourceReaderImpl()
+ {
+ super();
+ loggedException = null;
- Exception loggedException;
+ // open the stream to a server and then parse the result ...
+ }
- public DasSourceReaderImpl() {
- super();
- loggedException = null;
+ private InputStream open(URL url) throws java.io.IOException,
+ java.net.ConnectException
+ {
+ InputStream inStream = null;
- // open the stream to a server and then parse the result ...
- }
-
- private InputStream open(URL url)
- throws java.io.IOException, java.net.ConnectException
- {
- InputStream inStream = null;
+ HttpURLConnection huc = DAS_FeatureRetrieve.openHttpURLConnection(url);
+ inStream = huc.getInputStream();
- HttpURLConnection huc = DAS_FeatureRetrieve.openHttpURLConnection(url);
+ return inStream;
- inStream = huc.getInputStream();
+ }
- return inStream;
-
- }
+ public DasSource[] readDasSource(URL url)
+ {
+ DasSource[] sources = new DasSource[0];
+ try
+ {
+ InputStream stream = open(url);
- public DasSource[] readDasSource(URL url){
- DasSource[] sources = new DasSource[0];
-
- try {
- InputStream stream = open(url);
-
- sources = readDasSource(stream);
- } catch (Exception e){
- e.printStackTrace();
- loggedException = e;
- }
- return sources;
+ sources = readDasSource(stream);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ loggedException = e;
}
+ return sources;
+ }
- /** read a DAS2 sources response and return a list of DAS sources.
- *
- */
- public DasSource[] readDasSource(InputStream stream) {
-
- DasSource[] sources = new DasSource[0];
-
- try {
- SAXParserFactory spfactory =
- SAXParserFactory.newInstance();
-
- spfactory.setValidating(false);
-
- SAXParser saxParser = null ;
-
- try{
- saxParser =
- spfactory.newSAXParser();
- } catch (ParserConfigurationException e) {
- e.printStackTrace();
- loggedException = e;
- }
-
- String vali = System.getProperty("XMLVALIDATION");
-
- boolean validation = false ;
- if ( vali != null )
- if ( vali.equals("true") )
- validation = true ;
+ /**
+ * read a DAS2 sources response and return a list of DAS sources.
+ *
+ */
+ public DasSource[] readDasSource(InputStream stream)
+ {
+ DasSource[] sources = new DasSource[0];
- XMLReader xmlreader = saxParser.getXMLReader();
-
- //XMLReader xmlreader = XMLReaderFactory.createXMLReader();
- try {
- xmlreader.setFeature("http://xml.org/sax/features/validation", validation);
- } catch (SAXException e) {
- //logger.log(Level.FINE,"Cannot set validation " + validation);
- }
-
- try {
- xmlreader.setFeature("http://apache.org/xml/features/nonvalidating/load-external-dtd",validation);
- } catch (SAXNotRecognizedException e){
- e.printStackTrace();
- //logger.log(Level.FINE,"Cannot set load-external-dtd "+validation);
-
- }
-
- DAS2SourceHandler cont_handle = new DAS2SourceHandler() ;
-
- xmlreader.setContentHandler(cont_handle);
- xmlreader.setErrorHandler(new org.xml.sax.helpers.DefaultHandler());
- InputSource insource = new InputSource() ;
- insource.setByteStream(stream);
+ try
+ {
+ SAXParserFactory spfactory = SAXParserFactory.newInstance();
+ spfactory.setValidating(false);
- xmlreader.parse(insource);
- sources = cont_handle.getSources();
+ SAXParser saxParser = null;
+ try
+ {
+ saxParser = spfactory.newSAXParser();
+ } catch (ParserConfigurationException e)
+ {
+ e.printStackTrace();
+ loggedException = e;
+ }
+ String vali = System.getProperty("XMLVALIDATION");
- } catch (Exception e) {
- e.printStackTrace();
- loggedException = e;
+ boolean validation = false;
+ if (vali != null)
+ {
+ if (vali.equals("true"))
+ {
+ validation = true;
}
- return sources;
- }
-
- public Exception getLoggedException(){
- return loggedException;
+ }
+
+ XMLReader xmlreader = saxParser.getXMLReader();
+
+ // XMLReader xmlreader = XMLReaderFactory.createXMLReader();
+ try
+ {
+ xmlreader.setFeature("http://xml.org/sax/features/validation",
+ validation);
+ } catch (SAXException e)
+ {
+ // logger.log(Level.FINE,"Cannot set validation " + validation);
+ }
+
+ try
+ {
+ xmlreader
+ .setFeature(
+ "http://apache.org/xml/features/nonvalidating/load-external-dtd",
+ validation);
+ } catch (SAXNotRecognizedException e)
+ {
+ e.printStackTrace();
+ // logger.log(Level.FINE,"Cannot set load-external-dtd "+validation);
+
+ }
+
+ DAS2SourceHandler cont_handle = new DAS2SourceHandler();
+
+ xmlreader.setContentHandler(cont_handle);
+ xmlreader.setErrorHandler(new org.xml.sax.helpers.DefaultHandler());
+ InputSource insource = new InputSource();
+ insource.setByteStream(stream);
+
+ xmlreader.parse(insource);
+ sources = cont_handle.getSources();
+
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ loggedException = e;
}
-
- public static void main (String[] args){
- String url = "http://www.spice-3d.org/dasregistry/das2/sources/";
- DasSourceReaderImpl reader = new DasSourceReaderImpl();
- try {
- URL u = new URL(url);
- DasSource[] sources = reader.readDasSource(u);
- for (int i=0; i< sources.length;i++){
- DasSource ds = sources[i];
- System.out.println(ds.toString());
- }
-
- } catch (Exception e){
- e.printStackTrace();
- }
-
+ return sources;
+ }
+
+ public Exception getLoggedException()
+ {
+ return loggedException;
+ }
+
+ public static void main(String[] args)
+ {
+ String url = "http://www.spice-3d.org/dasregistry/das2/sources/";
+ DasSourceReaderImpl reader = new DasSourceReaderImpl();
+ try
+ {
+ URL u = new URL(url);
+ DasSource[] sources = reader.readDasSource(u);
+ for (int i = 0; i < sources.length; i++)
+ {
+ DasSource ds = sources[i];
+ System.out.println(ds.toString());
+ }
+
+ } catch (Exception e)
+ {
+ e.printStackTrace();
}
-
+ }
}
git://source.jalview.org / jalview.git / blobdiff