webservices/compbio/ws/server/RNAalifoldWS.java

   1 package compbio.ws.server;\r
   2 \r
   3 import java.util.List;\r
   4 \r
   5 import javax.jws.WebService;\r
   6 \r
   7 import org.apache.log4j.Logger;\r
   8 \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
  23 \r
  24 @WebService(endpointInterface = "compbio.data.msa.SequenceAnnotation", targetNamespace = JABAService.V2_SERVICE_NAMESPACE, serviceName = "RNAalifoldWS")\r
  25 public class RNAalifoldWS extends SequenceAnnotationService<RNAalifold> \r
  26                 implements\r
  27                         SequenceAnnotation<RNAalifold> {\r
  28 \r
  29         private static Logger log = Logger.getLogger(RNAalifoldWS.class);\r
  30         \r
  31         public RNAalifoldWS() {\r
  32                 super (new RNAalifold(), log);\r
  33         }\r
  34 \r
  35         \r
  36 //      // for testing\r
  37 //      @Override\r
  38 //      public RNAStructScoreManager getAnnotation(String jobId) \r
  39 //                      throws ResultNotAvailableException {\r
  40 //              return WSUtil.getAnnotation(jobId, log);\r
  41 //      }\r
  42         \r
  43         \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
  46         @Override\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
  53                                 getLimit(""));\r
  54         }\r
  55 \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
  58         @Override\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
  65                 \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
  70                                 getLimit(""));\r
  71         }\r
  72         \r
  73         \r
  74         /*\r
  75          * No presets are supported, thus the result of this call will be as simple\r
  76          * call to analize without parameters\r
  77          */\r
  78         @Override\r
  79         public String presetAnalize(List<FastaSequence> sequences,\r
  80                         Preset<RNAalifold> preset) throws UnsupportedRuntimeException,\r
  81                         LimitExceededException, JobSubmissionException,\r
  82                         WrongParameterException {\r
  83 \r
  84                 return analize(sequences);\r
  85         }\r
  86 }\r
  87         \r
  88         \r