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         // Only purpose is to replace "analize" with "fold" method \r
  36         // so that a clustal input file and not fasta will be generated\r
  37         @Override\r
  38         public String analize(List<FastaSequence> sequences)\r
  39                         throws UnsupportedRuntimeException, LimitExceededException,\r
  40                         JobSubmissionException {\r
  41                 WSUtil.validateFastaInput(sequences);\r
  42                 ConfiguredExecutable<RNAalifoldWS> confRNAalifold = init(sequences);\r
  43                 return WSUtil.fold(sequences, confRNAalifold, log, "analize",\r
  44                                 getLimit(""));\r
  45         }\r
  46 \r
  47         // Only purpose is to replace "analize" with "fold" method \r
  48                 // so that a clustal input file and not fasta will be generated\r
  49         @Override\r
  50         public String customAnalize(List<FastaSequence> sequences,\r
  51                         List<Option<RNAalifold>> options) throws UnsupportedRuntimeException,\r
  52                         LimitExceededException, JobSubmissionException,\r
  53                         WrongParameterException {\r
  54                 WSUtil.validateFastaInput(sequences);\r
  55                 ConfiguredExecutable<RNAalifold> confRNAalifold = init(sequences);\r
  56                 \r
  57                 List<String> params = WSUtil.getCommands(options,\r
  58                                 AACon.KEY_VALUE_SEPARATOR);\r
  59                 confRNAalifold.addParameters(params);\r
  60                 return WSUtil.fold(sequences, confRNAalifold, log, "customAnalize",\r
  61                                 getLimit(""));\r
  62         }\r
  63         \r
  64         \r
  65         /*\r
  66          * No presets are supported, thus the result of this call will be as simple\r
  67          * call to analize without parameters\r
  68          */\r
  69         @Override\r
  70         public String presetAnalize(List<FastaSequence> sequences,\r
  71                         Preset<RNAalifold> preset) throws UnsupportedRuntimeException,\r
  72                         LimitExceededException, JobSubmissionException,\r
  73                         WrongParameterException {\r
  74 \r
  75                 return analize(sequences);\r
  76         }\r
  77 }\r
  78         \r
  79         \r