*
*/
-package org.biojava.dasobert.das ;
+package org.biojava.dasobert.das;
-import java.util.*;
import java.net.*;
-import java.util.logging.* ;
-import org.biojava.dasobert.eventmodel.FeatureListener;
-import org.biojava.dasobert.eventmodel.FeatureEvent;
-import org.biojava.dasobert.dasregistry.Das1Source;
+import java.util.*;
+import java.util.logging.*;
+
+import org.biojava.dasobert.dasregistry.*;
+import org.biojava.dasobert.eventmodel.*;
/** a thread that connects to a DAS - Feature service and gets the features
*
implements Runnable
{
- /** number of times the client tries to reconnect to the server if a "come back later" is returned.
- * the server should provide a reasonable estimation how long it will take him to create results.
- * if this number of requests is still not successfull, give up.
- */
- public static int MAX_COME_BACK_ITERATIONS = 5;
-
- public static int MAX_NR_FEATURES = 300;
-
- static Logger logger = Logger.getLogger("org.biojava.spice");
-
- Das1Source dasSource;
- String ac ;
- List featureListeners;
- Thread thread;
-
- public FeatureThread (String accessionCode, Das1Source dasSource) {
- this.dasSource = dasSource;
- this.ac = accessionCode;
- featureListeners = new ArrayList();
- }
-
- public void addFeatureListener(FeatureListener li) {
- featureListeners.add(li);
- }
-
- public void clearFeatureListeners() {
- featureListeners.clear();
- }
-
- public synchronized void stop(){
- thread = null;
- notify();
- }
-
-
-
-
- public void run() {
- Thread me = Thread.currentThread();
- while ( thread == me) {
- String url = dasSource.getUrl();
- String queryString = url + "features?segment="+ ac ;
- URL cmd = null ;
- try {
- cmd = new URL(queryString);
- } catch (MalformedURLException e ) {
- logger.warning("got MalformedURL from das source " +dasSource);
- e.printStackTrace();
- }
+ /** number of times the client tries to reconnect to the server if a "come back later" is returned.
+ * the server should provide a reasonable estimation how long it will take him to create results.
+ * if this number of requests is still not successfull, give up.
+ */
+ public static int MAX_COME_BACK_ITERATIONS = 5;
+
+ public static int MAX_NR_FEATURES = 300;
+
+ static Logger logger = Logger.getLogger("org.biojava.spice");
+
+ Das1Source dasSource;
+ String ac;
+ List featureListeners;
+ Thread thread;
+
+ public FeatureThread(String accessionCode, Das1Source dasSource)
+ {
+ this.dasSource = dasSource;
+ this.ac = accessionCode;
+ featureListeners = new ArrayList();
+ }
+
+ public void addFeatureListener(FeatureListener li)
+ {
+ featureListeners.add(li);
+ }
+
+ public void clearFeatureListeners()
+ {
+ featureListeners.clear();
+ }
+
+ public synchronized void stop()
+ {
+ thread = null;
+ notify();
+ }
+
+ public void run()
+ {
+ Thread me = Thread.currentThread();
+ while (thread == me)
+ {
+ String url = dasSource.getUrl();
+ String queryString = url + "features?segment=" + ac;
+ URL cmd = null;
+ try
+ {
+ cmd = new URL(queryString);
+ }
+ catch (MalformedURLException e)
+ {
+ logger.warning("got MalformedURL from das source " + dasSource);
+ e.printStackTrace();
+
+ }
+
+ logger.info("requesting features from " + cmd);
+ DAS_FeatureRetrieve ftmp = new DAS_FeatureRetrieve(cmd);
+
+ int comeBackLater = ftmp.getComeBackLater();
+ int securityCounter = 0;
+ while ( (thread == me) && (comeBackLater > 0))
+ {
+ securityCounter++;
+ if (securityCounter >= MAX_COME_BACK_ITERATIONS)
+ {
+ comeBackLater = -1;
+ break;
- logger.info("requesting features from " + cmd);
- DAS_FeatureRetrieve ftmp = new DAS_FeatureRetrieve(cmd);
-
-
- int comeBackLater = ftmp.getComeBackLater();
- int securityCounter = 0;
- while ( (thread == me) && ( comeBackLater > 0 )) {
- securityCounter++;
- if ( securityCounter >= MAX_COME_BACK_ITERATIONS){
- comeBackLater = -1;
- break;
-
- }
- notifyComeBackLater(comeBackLater);
- // server is still calculating - asks us to come back later
- try {
- wait (comeBackLater);
- } catch (InterruptedException e){
- comeBackLater = -1;
- break;
- }
-
- ftmp.reload();
- comeBackLater = ftmp.getComeBackLater();
- }
-
- if ( ! (thread == me ) ) {
- break;
- }
-
- List features = ftmp.get_features();
-
- // a fallback mechanism to prevent DAS sources from bringing down spice
- if ( features.size() > MAX_NR_FEATURES){
- logger.warning("DAS source returned more than " + MAX_NR_FEATURES + "features. " +
- " throwing away excess features at " +cmd);
- features = features.subList(0,MAX_NR_FEATURES);
- }
+ }
+ notifyComeBackLater(comeBackLater);
+ // server is still calculating - asks us to come back later
+ try
+ {
+ wait(comeBackLater);
+ }
+ catch (InterruptedException e)
+ {
+ comeBackLater = -1;
+ break;
+ }
+ ftmp.reload();
+ comeBackLater = ftmp.getComeBackLater();
+ }
- // notify FeatureListeners
- Map[] feats = (Map[])features.toArray(new Map[features.size()]);
- notifyFeatureListeners(feats);
+ if (! (thread == me))
+ {
+ break;
+ }
- break;
+ List features = ftmp.get_features();
+ String version = ftmp.getVersion();
+ // a fallback mechanism to prevent DAS sources from bringing down spice
+ if (features.size() > MAX_NR_FEATURES)
+ {
+ logger.warning("DAS source returned more than " + MAX_NR_FEATURES +
+ "features. " +
+ " throwing away excess features at " + cmd);
+ features = features.subList(0, MAX_NR_FEATURES);
+ }
- }
- thread = null;
+ // notify FeatureListeners
+ Map[] feats = (Map[]) features.toArray(new Map[features.size()]);
+ notifyFeatureListeners(feats, version);
- }
+ break;
- public void start() {
- thread = new Thread(this);
- thread.start();
}
-
- private void notifyFeatureListeners(Map[] feats){
- logger.finest("FeatureThread found " + feats.length + " features");
- FeatureEvent fevent = new FeatureEvent(feats,dasSource);
- Iterator fiter = featureListeners.iterator();
- while (fiter.hasNext()){
- FeatureListener fi = (FeatureListener)fiter.next();
- fi.newFeatures(fevent);
- }
+ thread = null;
+
+ }
+
+ public void start()
+ {
+ thread = new Thread(this);
+ thread.start();
+ }
+
+ private void notifyFeatureListeners(Map[] feats, String version)
+ {
+ logger.finest("FeatureThread found " + feats.length + " features");
+ FeatureEvent fevent = new FeatureEvent(feats, dasSource, version);
+ Iterator fiter = featureListeners.iterator();
+ while (fiter.hasNext())
+ {
+ FeatureListener fi = (FeatureListener) fiter.next();
+ fi.newFeatures(fevent);
}
-
- /** the Annotation server requested to be queried again in a while
- *
- * @param comeBackLater
- */
- private void notifyComeBackLater(int comeBackLater){
- FeatureEvent event = new FeatureEvent(new HashMap[0],dasSource);
- event.setComeBackLater(comeBackLater);
- Iterator fiter = featureListeners.iterator();
- while (fiter.hasNext()){
- FeatureListener fi = (FeatureListener)fiter.next();
- fi.comeBackLater(event);
- }
-
+ }
+
+ /** the Annotation server requested to be queried again in a while
+ *
+ * @param comeBackLater
+ */
+ private void notifyComeBackLater(int comeBackLater)
+ {
+ FeatureEvent event = new FeatureEvent(new HashMap[0], dasSource, "");
+ event.setComeBackLater(comeBackLater);
+ Iterator fiter = featureListeners.iterator();
+ while (fiter.hasNext())
+ {
+ FeatureListener fi = (FeatureListener) fiter.next();
+ fi.comeBackLater(event);
}
+ }
}
-
git://source.jalview.org / jalview.git / blobdiff