/**
* A class to perform a DAS features request
- *
- * @author Andreas Prlic
- * Adapted for jalview use.
- * @author Andrew Waterhouse
- * Updated to Das 1.53e feature spec.
+ *
+ * @author Andreas Prlic Adapted for jalview use.
+ * @author Andrew Waterhouse Updated to Das 1.53e feature spec.
* @author Jim Procter
*/
public class DAS_FeatureRetrieve
{
String version;
+
List features;
+
Logger logger;
+
int comeBackLater;
+
URL url;
+
/**
- * @param url the URL the features should be downloaded from
- *
+ * @param url
+ * the URL the features should be downloaded from
+ *
*/
public DAS_FeatureRetrieve(URL url)
{
reload();
}
- /** contact the DAS-feature server again. Usually
- * it is not necessary to call this again, because the constructor already does, but
- * if comeBackLater > -1 this should be called again.
- *
+ /**
+ * contact the DAS-feature server again. Usually it is not necessary to call
+ * this again, because the constructor already does, but if comeBackLater > -1
+ * this should be called again.
+ *
*/
public void reload()
{
try
{
dasInStream = open(url);
- }
- catch (Exception e)
+ } catch (Exception e)
{
comeBackLater = -1;
System.out.println("NO RESPONSE FROM " + url);
return;
}
- SAXParserFactory spfactory =
- SAXParserFactory.newInstance();
+ SAXParserFactory spfactory = SAXParserFactory.newInstance();
spfactory.setValidating(false);
try
{
- saxParser =
- spfactory.newSAXParser();
- }
- catch (ParserConfigurationException e)
+ saxParser = spfactory.newSAXParser();
+ } catch (ParserConfigurationException e)
{
e.printStackTrace();
}
XMLReader xmlreader = saxParser.getXMLReader();
- //XMLReader xmlreader = XMLReaderFactory.createXMLReader();
+ // XMLReader xmlreader = XMLReaderFactory.createXMLReader();
try
{
xmlreader.setFeature("http://xml.org/sax/features/validation",
- validation);
- }
- catch (SAXException e)
+ 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)
+ 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);
+ logger
+ .log(Level.FINE, "Cannot set load-external-dtd "
+ + validation);
}
{
xmlreader.parse(insource);
features = cont_handle.get_features();
- version = cont_handle.getVersion();
-
+ version = cont_handle.getVersion();
+
comeBackLater = cont_handle.getComBackLater();
- }
- catch (Exception e)
+ } catch (Exception e)
{
- System.out.println("Error parsing response from: " + url + "\n" + e);
+ System.out
+ .println("Error parsing response from: " + url + "\n" + e);
logger.log(Level.FINE, "error while parsing response from " + url);
comeBackLater = -1;
features = new ArrayList();
}
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
ex.printStackTrace();
comeBackLater = -1;
}
}
- /** open HttpURLConnection. Recommended way to open
- * HttpURLConnections, since this take care of setting timeouts
- * properly for java 1.4 and 1.5*/
+ /**
+ * open HttpURLConnection. Recommended way to open HttpURLConnections, since
+ * this take care of setting timeouts properly for java 1.4 and 1.5
+ */
public static HttpURLConnection openHttpURLConnection(URL url)
- throws IOException, ConnectException
+ throws IOException, ConnectException
{
HttpURLConnection huc = null;
huc = (HttpURLConnection) url.openConnection();
String os_arch = java.lang.System.getProperty("os.arch");
String VERSION = "1.0";
- String userAgent = "Jalview " + VERSION + "(" + os_name + "; " + os_arch +
- " ; " + os_version + ")";
- //e.g. "Mozilla/5.0 (Windows; U; Win98; en-US; rv:1.7.2) Gecko/20040803"
+ String userAgent = "Jalview " + VERSION + "(" + os_name + "; "
+ + os_arch + " ; " + os_version + ")";
+ // e.g. "Mozilla/5.0 (Windows; U; Win98; en-US; rv:1.7.2) Gecko/20040803"
huc.addRequestProperty("User-Agent", userAgent);
- //logger.finest("opening "+url);
-
+ // logger.finest("opening "+url);
int timeout = 10000;
- System.setProperty("sun.net.client.defaultConnectTimeout", timeout + "");
+ System
+ .setProperty("sun.net.client.defaultConnectTimeout", timeout
+ + "");
System.setProperty("sun.net.client.defaultReadTimeout", timeout + "");
- // use reflection to determine if get and set timeout methods for urlconnection are available
+ // use reflection to determine if get and set timeout methods for
+ // urlconnection are available
// seems java 1.5 does not watch the System properties any longer...
// and java 1.4 did not provide these...
// for 1.4 see setSystemProperties
try
{
// try to use reflection to set timeout property
- Class urlconnectionClass = Class.forName("java.net.HttpURLConnection");
+ Class urlconnectionClass = Class
+ .forName("java.net.HttpURLConnection");
Method setconnecttimeout = urlconnectionClass.getMethod(
- "setConnectTimeout", new Class[]
- {int.class}
- );
+ "setConnectTimeout", new Class[]
+ { int.class });
setconnecttimeout.invoke(huc, new Object[]
- {new Integer(timeout)});
+ { new Integer(timeout) });
Method setreadtimeout = urlconnectionClass.getMethod(
- "setReadTimeout", new Class[]
- {int.class}
- );
+ "setReadTimeout", new Class[]
+ { int.class });
setreadtimeout.invoke(huc, new Object[]
- {new Integer(timeout)});
- //System.out.println("successfully set java 1.5 timeout");
- }
- catch (Exception e)
+ { new Integer(timeout) });
+ // System.out.println("successfully set java 1.5 timeout");
+ } catch (Exception e)
{
- //e.printStackTrace();
+ // e.printStackTrace();
// most likely it was a NoSuchMEthodException and we are running java 1.4.
}
return huc;
}
- private InputStream open(URL url)
- throws java.io.IOException, java.net.ConnectException
+ private InputStream open(URL url) throws java.io.IOException,
+ java.net.ConnectException
{
InputStream inStream = null;
}
- /** returns a List of Features
- * @return a List of Maps containing the features*/
+ /**
+ * returns a List of Features
+ *
+ * @return a List of Maps containing the features
+ */
public List get_features()
{
return features;
- }
-
-
- /** Get the version string of the reference object.
- * If it does not match the version string that is obtained from the
- * reference server there is a version problem!
- *
- * @return version string. (e.g. a MD5 digest of the reference sequence)
- */
- public String getVersion() {
- return version;
- }
-
-
- public void setVersion(String version) {
- this.version = version;
}
- /** returns the comeBackLater value - if a server returned suchh -
- *
+ /**
+ * Get the version string of the reference object. If it does not match the
+ * version string that is obtained from the reference server there is a
+ * version problem!
+ *
+ * @return version string. (e.g. a MD5 digest of the reference sequence)
+ */
+ public String getVersion()
+ {
+ return version;
+ }
+
+ public void setVersion(String version)
+ {
+ this.version = version;
+ }
+
+ /**
+ * returns the comeBackLater value - if a server returned suchh -
+ *
* @return comeBackLater in seconds, or -1 if not provided by server
*/
public int getComeBackLater()
git://source.jalview.org / jalview.git / blobdiff