1 package compbio.ws.server;
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3 import java.util.List;
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5 import javax.jws.WebService;
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7 import org.apache.log4j.Logger;
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9 import compbio.data.msa.JABAService;
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10 import compbio.data.msa.SequenceAnnotation;
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11 import compbio.data.sequence.FastaSequence;
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12 import compbio.data.sequence.RNAStructScoreManager;
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13 import compbio.engine.client.ConfiguredExecutable;
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14 import compbio.metadata.JobSubmissionException;
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15 import compbio.metadata.LimitExceededException;
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16 import compbio.metadata.Option;
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17 import compbio.metadata.Preset;
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18 import compbio.metadata.ResultNotAvailableException;
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19 import compbio.metadata.UnsupportedRuntimeException;
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20 import compbio.metadata.WrongParameterException;
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21 import compbio.runner.conservation.AACon;
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22 import compbio.runner.structure.RNAalifold;
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24 @WebService(endpointInterface = "compbio.data.msa.SequenceAnnotation", targetNamespace = JABAService.V2_SERVICE_NAMESPACE, serviceName = "RNAalifoldWS")
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25 public class RNAalifoldWS extends SequenceAnnotationService<RNAalifold>
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27 SequenceAnnotation<RNAalifold> {
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29 private static Logger log = Logger.getLogger(RNAalifoldWS.class);
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31 public RNAalifoldWS() {
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32 super (new RNAalifold(), log);
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35 // Only purpose is to replace "analize" with "fold" method
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36 // so that a clustal input file and not fasta will be generated
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38 public String analize(List<FastaSequence> sequences)
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39 throws UnsupportedRuntimeException, LimitExceededException,
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40 JobSubmissionException {
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41 WSUtil.validateFastaInput(sequences);
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42 ConfiguredExecutable<RNAalifoldWS> confRNAalifold = init(sequences);
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43 return WSUtil.fold(sequences, confRNAalifold, log, "analize",
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47 // Only purpose is to replace "analize" with "fold" method
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48 // so that a clustal input file and not fasta will be generated
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50 public String customAnalize(List<FastaSequence> sequences,
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51 List<Option<RNAalifold>> options) throws UnsupportedRuntimeException,
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52 LimitExceededException, JobSubmissionException,
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53 WrongParameterException {
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54 WSUtil.validateFastaInput(sequences);
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55 ConfiguredExecutable<RNAalifold> confRNAalifold = init(sequences);
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57 List<String> params = WSUtil.getCommands(options,
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58 AACon.KEY_VALUE_SEPARATOR);
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59 confRNAalifold.addParameters(params);
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60 return WSUtil.fold(sequences, confRNAalifold, log, "customAnalize",
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66 * No presets are supported, thus the result of this call will be as simple
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67 * call to analize without parameters
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70 public String presetAnalize(List<FastaSequence> sequences,
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71 Preset<RNAalifold> preset) throws UnsupportedRuntimeException,
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72 LimitExceededException, JobSubmissionException,
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73 WrongParameterException {
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75 return analize(sequences);
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