webservices/compbio/ws/server/RNAalifoldWS.java

   1 package compbio.ws.server;
   2
   3 import java.io.File;
   4 import java.util.List;
   5
   6 import javax.jws.WebParam;
   7 import javax.jws.WebService;
   8
   9 import org.apache.log4j.Logger;
  10
  11 import compbio.data.msa.FoldWS;
  12 import compbio.data.msa.JABAService;
  13 import compbio.data.msa.JManagement;
  14 import compbio.data.msa.Metadata;
  15 import compbio.data.msa.SequenceAnnotation;
  16 import compbio.data.sequence.Alignment;
  17 import compbio.data.sequence.RNAStruct;
  18 import compbio.data.sequence.FastaSequence;
  19 import compbio.engine.AsyncExecutor;
  20 import compbio.engine.Configurator;
  21 import compbio.engine.client.ConfiguredExecutable;
  22 import compbio.engine.client.SkeletalExecutable;
  23 import compbio.metadata.ChunkHolder;
  24 import compbio.metadata.JobStatus;
  25 import compbio.metadata.JobSubmissionException;
  26 import compbio.metadata.Limit;
  27 import compbio.metadata.LimitExceededException;
  28 import compbio.metadata.LimitsManager;
  29 import compbio.metadata.Option;
  30 import compbio.metadata.Preset;
  31 import compbio.metadata.PresetManager;
  32 import compbio.metadata.ResultNotAvailableException;
  33 import compbio.metadata.RunnerConfig;
  34 import compbio.metadata.UnsupportedRuntimeException;
  35 import compbio.metadata.WrongParameterException;
  36 import compbio.runner.Util;
  37 import compbio.runner.disorder.GlobPlot;
  38 import compbio.runner.structure.RNAalifold;
  39
  40 @WebService(endpointInterface = "compbio.data.msa.SequenceAnnotation", targetNamespace = JABAService.V2_SERVICE_NAMESPACE, serviceName = "RNAalifoldWS")
  41 public class RNAalifoldWS extends SequenceAnnotationService<RNAalifold>
  42                 implements
  43                         SequenceAnnotation<RNAalifold> {
  44
  45         private static Logger log = Logger.getLogger(ClustalWS.class);
  46
  47         public RNAalifoldWS() {
  48                 super (new RNAalifold(), log);
  49         }
  50
  51         /*
  52          * No options are supported, thus the result of this call will be as simple
  53          * call to analize without parameters
  54          */
  55         @Override
  56         public String customAnalize(List<FastaSequence> sequences,
  57                         List<Option<RNAalifold>> options) throws UnsupportedRuntimeException,
  58                         LimitExceededException, JobSubmissionException,
  59                         WrongParameterException {
  60
  61                 return analize(sequences);
  62         }
  63
  64         /*
  65          * No presets are supported, thus the result of this call will be as simple
  66          * call to analize without parameters
  67          */
  68         @Override
  69         public String presetAnalize(List<FastaSequence> sequences,
  70                         Preset<RNAalifold> preset) throws UnsupportedRuntimeException,
  71                         LimitExceededException, JobSubmissionException,
  72                         WrongParameterException {
  73
  74                 return analize(sequences);
  75         }
  76 }
  77
  78