\r
import java.io.File;\r
import java.util.Arrays;\r
-import java.util.HashSet;\r
import java.util.List;\r
\r
import javax.annotation.Resource;\r
\r
import org.apache.log4j.Logger;\r
\r
-import compbio.data.msa.Annotation;\r
+import compbio.data.msa.SequenceAnnotation;\r
import compbio.data.sequence.FastaSequence;\r
-import compbio.data.sequence.Score;\r
+import compbio.data.sequence.ScoreManager;\r
import compbio.engine.AsyncExecutor;\r
import compbio.engine.Configurator;\r
import compbio.engine.client.ConfiguredExecutable;\r
+import compbio.engine.client.SkeletalExecutable;\r
import compbio.metadata.ChunkHolder;\r
import compbio.metadata.JobStatus;\r
import compbio.metadata.JobSubmissionException;\r
import compbio.runner.Util;\r
import compbio.runner.conservation.AACon;\r
\r
-@WebService(endpointInterface = "compbio.data.msa.Annotation", targetNamespace = "http://msa.data.compbio/01/12/2010/", serviceName = "AAConWS")\r
-public class AAConWS implements Annotation<AACon> {\r
+@WebService(endpointInterface = "compbio.data.msa.SequenceAnnotation", targetNamespace = "http://msa.data.compbio/01/12/2010/", serviceName = "AAConWS")\r
+public class AAConWS implements SequenceAnnotation<AACon> {\r
\r
// Ask for resource injection\r
@Resource\r
private static final PresetManager<AACon> aaconPresets = Util\r
.getPresets(AACon.class);\r
\r
+ private static final LimitsManager<AACon> limitMan = compbio.engine.client.Util\r
+ .getLimits(new AACon().getType());\r
+\r
ConfiguredExecutable<AACon> init(List<FastaSequence> sequences)\r
throws JobSubmissionException {\r
AACon aacon = new AACon();\r
- aacon.setInput("fasta.in").setOutput("aacon.out");\r
+ aacon.setInput(SkeletalExecutable.INPUT).setOutput(\r
+ SkeletalExecutable.OUTPUT);\r
return Configurator.configureExecutable(aacon, sequences);\r
}\r
\r
@Override\r
- public HashSet<Score> getConservation(String jobId)\r
+ public ScoreManager getAnnotation(String jobId)\r
throws ResultNotAvailableException {\r
WSUtil.validateJobId(jobId);\r
AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
ConfiguredExecutable<AACon> aacon = (ConfiguredExecutable<AACon>) asyncEngine\r
.getResults(jobId);\r
- HashSet<Score> mas = aacon.getResults();\r
- log.info(jobId + " getConservation : " + mas);\r
+ ScoreManager mas = aacon.getResults();\r
+ log.trace(jobId + " getConservation : " + mas);\r
return mas;\r
}\r
/*\r
\r
@Override\r
public Limit<AACon> getLimit(String presetName) {\r
- return new AACon().getLimit(presetName);\r
+ if (limitMan == null) {\r
+ // Limit is not defined\r
+ return null;\r
+ }\r
+ return limitMan.getLimitByName(presetName);\r
}\r
\r
@Override\r
public LimitsManager<AACon> getLimits() {\r
- return new AACon().getLimits();\r
+ return limitMan;\r
}\r
\r
@Override\r