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> implements SequenceAnnotation<RNAalifold> {\r
  24 \r
  25         private static Logger log = Logger.getLogger(RNAalifoldWS.class);\r
  26         \r
  27         public RNAalifoldWS() {\r
  28                 super (new RNAalifold(), log);\r
  29         }\r
  30         \r
  31         // Only purpose is to replace "analize" with "fold" method \r
  32         // so that a clustal input file and not fasta will be generated\r
  33         @SuppressWarnings("unchecked")\r
  34         @Override\r
  35         public String analize(List<FastaSequence> sequences)\r
  36                         throws UnsupportedRuntimeException, LimitExceededException,\r
  37                         JobSubmissionException {\r
  38                 WSUtil.validateFastaInput(sequences);\r
  39                 ConfiguredExecutable<RNAalifoldWS> confRNAalifold = init(sequences);\r
  40                 return WSUtil.fold(sequences, confRNAalifold, log, "analize", getLimit(""));\r
  41         }\r
  42 \r
  43         // Only purpose is to replace "analize" with "fold" method \r
  44         // so that a clustal input file and not fasta will be generated\r
  45         @SuppressWarnings("unchecked")\r
  46         @Override\r
  47         public String customAnalize(List<FastaSequence> sequences,\r
  48                         List<Option<RNAalifold>> options) throws UnsupportedRuntimeException,\r
  49                         LimitExceededException, JobSubmissionException,\r
  50                         WrongParameterException {\r
  51                 WSUtil.validateFastaInput(sequences);\r
  52                 ConfiguredExecutable<RNAalifold> confRNAalifold = init(sequences);\r
  53                 List<String> params = WSUtil.getCommands(options, RNAalifold.KEY_VALUE_SEPARATOR);\r
  54                 confRNAalifold.addParameters(params);\r
  55                 return WSUtil.fold(sequences, confRNAalifold, log, "customAnalize", getLimit(""));\r
  56         }\r
  57         \r
  58         \r
  59         /*\r
  60          * No presets are supported, thus the result of this call will be as simple\r
  61          * call to analize without parameters\r
  62          */\r
  63         @Override\r
  64         public String presetAnalize(List<FastaSequence> sequences,\r
  65                         Preset<RNAalifold> preset) throws UnsupportedRuntimeException,\r
  66                         LimitExceededException, JobSubmissionException,\r
  67                         WrongParameterException {\r
  68                 return analize(sequences);\r
  69         }\r
  70 }\r