\r
import java.io.File;\r
import java.util.Arrays;\r
-import java.util.HashMap;\r
import java.util.HashSet;\r
import java.util.List;\r
\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
private static final PresetManager<AACon> aaconPresets = Util\r
.getPresets(AACon.class);\r
\r
+ private static final LimitsManager<AACon> limitMan = compbio.runner.Util\r
+ .getLimits(new AACon().getType());\r
+\r
ConfiguredExecutable<AACon> init(List<FastaSequence> sequences)\r
throws JobSubmissionException {\r
AACon aacon = new AACon();\r
}\r
\r
@Override\r
- public HashMap<String, HashSet<Score>> getAnnotation(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
- HashMap<String, HashSet<Score>> result = new HashMap<String, HashSet<Score>>();\r
- result.put("Alignment", mas);\r
+ // ScoreManager result = new HashMap<String, HashSet<Score>>();\r
+ // result.put("Alignment", mas);\r
log.trace(jobId + " getConservation : " + mas);\r
- return result;\r
+ // FIXME\r
+ return null;\r
}\r
/*\r
* @SuppressWarnings("unchecked") public JalviewAnnotation\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