webservices/compbio/ws/server/SequenceAnnotationService.java

   1 package compbio.ws.server;\r
   2 \r
   3 import java.util.List;\r
   4 \r
   5 import org.apache.log4j.Logger;\r
   6 \r
   7 import compbio.data.sequence.FastaSequence;\r
   8 import compbio.data.sequence.ScoreManager;\r
   9 import compbio.engine.client.ConfiguredExecutable;\r
  10 import compbio.engine.client.SkeletalExecutable;\r
  11 import compbio.metadata.JobSubmissionException;\r
  12 import compbio.metadata.Limit;\r
  13 import compbio.metadata.LimitExceededException;\r
  14 import compbio.metadata.Option;\r
  15 import compbio.metadata.Preset;\r
  16 import compbio.metadata.ResultNotAvailableException;\r
  17 import compbio.metadata.UnsupportedRuntimeException;\r
  18 import compbio.metadata.WrongParameterException;\r
  19 import compbio.runner.conservation.AACon;\r
  20 \r
  21 /**\r
  22  * Common methods for all SequenceAnnotation web services\r
  23  * \r
  24  * @author pvtroshin\r
  25  * \r
  26  * @param <T>\r
  27  * \r
  28  * @version 1.0 June 2011\r
  29  * @since 2.0\r
  30  */\r
  31 public abstract class SequenceAnnotationService<T> extends GenericMetadataService {\r
  32 \r
  33         /*\r
  34          * FIXME - instances of the Runner (?) and their types should be defined in\r
  35          * Executable IF\r
  36          */\r
  37         SequenceAnnotationService(SkeletalExecutable<T> exec, Logger log) {\r
  38                 super(exec, log);\r
  39         }\r
  40 \r
  41         public ScoreManager getAnnotation(String jobId)\r
  42                         throws ResultNotAvailableException {\r
  43                 return WSUtil.getAnnotation(jobId, log);\r
  44         }\r
  45 \r
  46         public String analize(List<FastaSequence> sequences)\r
  47                         throws UnsupportedRuntimeException, LimitExceededException,\r
  48                         JobSubmissionException {\r
  49                 WSUtil.validateFastaInput(sequences);\r
  50                 ConfiguredExecutable<T> confIUPred = init(sequences);\r
  51                 return WSUtil.analize(sequences, confIUPred, log, "analize",\r
  52                                 getLimit(""));\r
  53         }\r
  54 \r
  55         public String customAnalize(List<FastaSequence> sequences,\r
  56                         List<Option<T>> options) throws UnsupportedRuntimeException,\r
  57                         LimitExceededException, JobSubmissionException,\r
  58                         WrongParameterException {\r
  59                 WSUtil.validateAAConInput(sequences);\r
  60                 ConfiguredExecutable<T> confAACon = init(sequences);\r
  61                 // Could not do that! Space separated values\r
  62                 // will all be treated as keys! thus duplicates removed\r
  63                 // String params = cbuilder.getCommand();\r
  64                 List<String> params = WSUtil.getCommands(options,\r
  65                                 AACon.KEY_VALUE_SEPARATOR);\r
  66                 confAACon.addParameters(params);\r
  67                 return WSUtil.analize(sequences, confAACon, log, "customAnalize",\r
  68                                 getLimit(""));\r
  69         }\r
  70 \r
  71         public String presetAnalize(List<FastaSequence> sequences, Preset<T> preset)\r
  72                         throws UnsupportedRuntimeException, LimitExceededException,\r
  73                         JobSubmissionException, WrongParameterException {\r
  74                 WSUtil.validateAAConInput(sequences);\r
  75                 if (preset == null) {\r
  76                         throw new WrongParameterException("Preset must be provided!");\r
  77                 }\r
  78                 ConfiguredExecutable<T> confAAcon = init(sequences);\r
  79                 confAAcon.addParameters(preset.getOptions());\r
  80                 Limit<T> limit = getLimit(preset.getName());\r
  81                 return WSUtil\r
  82                                 .analize(sequences, confAAcon, log, "presetAnalize", limit);\r
  83         }\r
  84 \r
  85 }\r