\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 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
ConfiguredExecutable<AACon> init(List<FastaSequence> sequences)\r
throws JobSubmissionException {\r
AACon aacon = new AACon();\r
+ aacon.setInput(SkeletalExecutable.INPUT).setOutput(\r
+ SkeletalExecutable.OUTPUT);\r
return Configurator.configureExecutable(aacon, sequences);\r
}\r
\r
AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
ConfiguredExecutable<AACon> aacon = (ConfiguredExecutable<AACon>) asyncEngine\r
.getResults(jobId);\r
- HashSet<Score> mas = aacon.getResults();\r
- // ScoreManager result = new HashMap<String, HashSet<Score>>();\r
- // result.put("Alignment", mas);\r
+ ScoreManager mas = aacon.getResults();\r
log.trace(jobId + " getConservation : " + mas);\r
- // FIXME\r
- return null;\r
+ return mas;\r
}\r
/*\r
* @SuppressWarnings("unchecked") public JalviewAnnotation\r