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