X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Forg%2Fbiojava%2Fdasobert%2Fdas2%2Fio%2FDasSourceReaderImpl.java;h=6b6122af6203d1618ba5aaffc9b1e6239fa6612f;hb=506d60f0e188723ddc91c26824b41ac7034df3fe;hp=3f0a07aa7253a526abeec7eee836808e9a321c22;hpb=714ad67911cdd8e2078cd3e961b5d709f5f0e5ce;p=jalview.git

diff --git a/src/org/biojava/dasobert/das2/io/DasSourceReaderImpl.java b/src/org/biojava/dasobert/das2/io/DasSourceReaderImpl.java
index 3f0a07a..6b6122a 100755
--- a/src/org/biojava/dasobert/das2/io/DasSourceReaderImpl.java
+++ b/src/org/biojava/dasobert/das2/io/DasSourceReaderImpl.java
@@ -22,152 +22,161 @@
  */
 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();
     }
 
-
+  }
 
 }