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.engine.client.ConfiguredExecutable;\r
  13 import compbio.metadata.JobSubmissionException;\r
  14 import compbio.metadata.LimitExceededException;\r
  15 import compbio.metadata.Option;\r
  16 import compbio.metadata.Preset;\r
  17 import compbio.metadata.UnsupportedRuntimeException;\r
  18 import compbio.metadata.WrongParameterException;\r
  19 import compbio.runner.conservation.AACon;\r
  20 import compbio.runner.structure.RNAalifold;\r
  21 \r
  22 @WebService(endpointInterface = "compbio.data.msa.SequenceAnnotation", targetNamespace = JABAService.V2_SERVICE_NAMESPACE, serviceName = "RNAalifoldWS")\r
  23 public class RNAalifoldWS extends SequenceAnnotationService<RNAalifold> \r
  24                 implements\r
  25                         SequenceAnnotation<RNAalifold> {\r
  26 \r
  27         private static Logger log = Logger.getLogger(RNAalifoldWS.class);\r
  28         \r
  29         public RNAalifoldWS() {\r
  30                 super (new RNAalifold(), log);\r
  31         }\r
  32         \r
  33         // Only purpose is to replace "analize" with "fold" method \r
  34         // so that a clustal input file and not fasta will be generated\r
  35         @Override\r
  36         public String analize(List<FastaSequence> sequences)\r
  37                         throws UnsupportedRuntimeException, LimitExceededException,\r
  38                         JobSubmissionException {\r
  39                 WSUtil.validateFastaInput(sequences);\r
  40                 ConfiguredExecutable<RNAalifoldWS> confRNAalifold = init(sequences);\r
  41                 return WSUtil.fold(sequences, confRNAalifold, log, "analize",\r
  42                                 getLimit(""));\r
  43         }\r
  44 \r
  45         // Only purpose is to replace "analize" with "fold" method \r
  46         // so that a clustal input file and not fasta will be generated\r
  47         @Override\r
  48         public String customAnalize(List<FastaSequence> sequences,\r
  49                         List<Option<RNAalifold>> options) throws UnsupportedRuntimeException,\r
  50                         LimitExceededException, JobSubmissionException,\r
  51                         WrongParameterException {\r
  52                 WSUtil.validateFastaInput(sequences);\r
  53                 ConfiguredExecutable<RNAalifold> confRNAalifold = init(sequences);\r
  54                 \r
  55                 List<String> params = WSUtil.getCommands(options,\r
  56                                 AACon.KEY_VALUE_SEPARATOR);\r
  57                 confRNAalifold.addParameters(params);\r
  58                 return WSUtil.fold(sequences, confRNAalifold, log, "customAnalize",\r
  59                                 getLimit(""));\r
  60         }\r
  61         \r
  62         \r
  63         /*\r
  64          * No presets are supported, thus the result of this call will be as simple\r
  65          * call to analize without parameters\r
  66          */\r
  67         @Override\r
  68         public String presetAnalize(List<FastaSequence> sequences,\r
  69                         Preset<RNAalifold> preset) throws UnsupportedRuntimeException,\r
  70                         LimitExceededException, JobSubmissionException,\r
  71                         WrongParameterException {\r
  72 \r
  73                 return analize(sequences);\r
  74         }\r
  75 }\r
  76         \r
  77         \r