1 /* Copyright (c) 2011 Peter Troshin
\r
3 * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0
\r
5 * This library is free software; you can redistribute it and/or modify it under the terms of the
\r
6 * Apache License version 2 as published by the Apache Software Foundation
\r
8 * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
\r
9 * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache
\r
10 * License for more details.
\r
12 * A copy of the license is in apache_license.txt. It is also available here:
\r
13 * @see: http://www.apache.org/licenses/LICENSE-2.0.txt
\r
15 * Any republication or derived work distributed in source code form
\r
16 * must include this copyright and license notice.
\r
18 package compbio.ws.server;
\r
20 import java.io.File;
\r
21 import java.util.Arrays;
\r
22 import java.util.List;
\r
24 import javax.jws.WebService;
\r
26 import org.apache.log4j.Logger;
\r
28 import compbio.data.msa.JABAService;
\r
29 import compbio.data.msa.SequenceAnnotation;
\r
30 import compbio.data.sequence.FastaSequence;
\r
31 import compbio.engine.Configurator;
\r
32 import compbio.engine.client.ConfiguredExecutable;
\r
33 import compbio.metadata.ChunkHolder;
\r
34 import compbio.metadata.JobSubmissionException;
\r
35 import compbio.metadata.LimitExceededException;
\r
36 import compbio.metadata.Option;
\r
37 import compbio.metadata.Preset;
\r
38 import compbio.metadata.UnsupportedRuntimeException;
\r
39 import compbio.metadata.WrongParameterException;
\r
40 import compbio.runner.conservation.AACon;
\r
42 @WebService(endpointInterface = "compbio.data.msa.SequenceAnnotation", targetNamespace = JABAService.V2_SERVICE_NAMESPACE, serviceName = "AAConWS")
\r
43 public class AAConWS extends SequenceAnnotationService<AACon>
\r
45 SequenceAnnotation<AACon> {
\r
47 private static Logger log = Logger.getLogger(AAConWS.class);
\r
50 super(new AACon(), log);
\r
54 * @SuppressWarnings("unchecked") public JalviewAnnotation
\r
55 * getJalviewAnnotation(String jobId) throws ResultNotAvailableException {
\r
56 * MultiAnnotatedSequence<Method> result = getResult(jobId); // TODO //
\r
57 * log(jobId, "getResults"); return result.toJalviewAnnotation(); }
\r
61 public String analize(List<FastaSequence> sequences)
\r
62 throws UnsupportedRuntimeException, LimitExceededException,
\r
63 JobSubmissionException {
\r
64 WSUtil.validateAAConInput(sequences);
\r
65 ConfiguredExecutable<AACon> confAAcon = init(sequences);
\r
67 // set default conservation method to fastest - SHENKIN
\r
68 // TODO: This violates encapsulation, should be moved to the runners
\r
70 confAAcon.addParameters(Arrays.asList("-m=SHENKIN"));
\r
71 return WSUtil.analize(sequences, confAAcon, log, "AAConWS analize",
\r
76 public String customAnalize(List<FastaSequence> sequences,
\r
77 List<Option<AACon>> options) throws UnsupportedRuntimeException,
\r
78 LimitExceededException, JobSubmissionException,
\r
79 WrongParameterException {
\r
80 WSUtil.validateAAConInput(sequences);
\r
81 return super.customAnalize(sequences, options);
\r
85 public String presetAnalize(List<FastaSequence> sequences,
\r
86 Preset<AACon> preset) throws UnsupportedRuntimeException,
\r
87 LimitExceededException, JobSubmissionException,
\r
88 WrongParameterException {
\r
89 WSUtil.validateAAConInput(sequences);
\r
90 return super.presetAnalize(sequences, preset);
\r
94 public ChunkHolder pullExecStatistics(String jobId, long position) {
\r
95 WSUtil.validateJobId(jobId);
\r
96 String file = Configurator.getWorkDirectory(jobId) + File.separator
\r
97 + AACon.getStatFile();
\r
98 return WSUtil.pullFile(file, position);
\r