1 package compbio.ws.server;
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4 import java.util.Arrays;
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5 import java.util.List;
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7 import javax.jws.WebService;
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9 import org.apache.log4j.Logger;
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11 import compbio.data.msa.JABAService;
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12 import compbio.data.msa.SequenceAnnotation;
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13 import compbio.data.sequence.FastaSequence;
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14 import compbio.engine.Configurator;
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15 import compbio.engine.client.ConfiguredExecutable;
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16 import compbio.metadata.ChunkHolder;
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17 import compbio.metadata.JobSubmissionException;
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18 import compbio.metadata.LimitExceededException;
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19 import compbio.metadata.UnsupportedRuntimeException;
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20 import compbio.runner.conservation.AACon;
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22 @WebService(endpointInterface = "compbio.data.msa.SequenceAnnotation", targetNamespace = JABAService.V2_SERVICE_NAMESPACE, serviceName = "AAConWS")
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23 public class AAConWS extends SequenceAnnotationService<AACon>
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25 SequenceAnnotation<AACon> {
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27 private static Logger log = Logger.getLogger(AAConWS.class);
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30 super(new AACon(), log);
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34 * @SuppressWarnings("unchecked") public JalviewAnnotation
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35 * getJalviewAnnotation(String jobId) throws ResultNotAvailableException {
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36 * MultiAnnotatedSequence<Method> result = getResult(jobId); // TODO //
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37 * log(jobId, "getResults"); return result.toJalviewAnnotation(); }
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41 public String analize(List<FastaSequence> sequences)
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42 throws UnsupportedRuntimeException, LimitExceededException,
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43 JobSubmissionException {
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44 WSUtil.validateAAConInput(sequences);
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45 ConfiguredExecutable<AACon> confAAcon = init(sequences);
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47 // set default conservation method to fastest - SHENKIN
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48 // TODO: This violates encapsulation, should be moved to the runners
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50 confAAcon.addParameters(Arrays.asList("-m=SHENKIN"));
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51 return WSUtil.analize(sequences, confAAcon, log, "AAConWS analize",
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56 public ChunkHolder pullExecStatistics(String jobId, long position) {
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57 WSUtil.validateJobId(jobId);
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58 String file = Configurator.getWorkDirectory(jobId) + File.separator
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59 + AACon.getStatFile();
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60 return WSUtil.pullFile(file, position);
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