webservices/compbio/ws/server/AAConWS.java

   1 package compbio.ws.server;\r
   2 \r
   3 import java.io.File;\r
   4 import java.util.Arrays;\r
   5 import java.util.List;\r
   6 \r
   7 import javax.jws.WebService;\r
   8 \r
   9 import org.apache.log4j.Logger;\r
  10 \r
  11 import compbio.data.msa.JABAService;\r
  12 import compbio.data.msa.SequenceAnnotation;\r
  13 import compbio.data.sequence.FastaSequence;\r
  14 import compbio.engine.Configurator;\r
  15 import compbio.engine.client.ConfiguredExecutable;\r
  16 import compbio.metadata.ChunkHolder;\r
  17 import compbio.metadata.JobSubmissionException;\r
  18 import compbio.metadata.LimitExceededException;\r
  19 import compbio.metadata.UnsupportedRuntimeException;\r
  20 import compbio.runner.conservation.AACon;\r
  21 \r
  22 @WebService(endpointInterface = "compbio.data.msa.SequenceAnnotation", targetNamespace = JABAService.V2_SERVICE_NAMESPACE, serviceName = "AAConWS")\r
  23 public class AAConWS extends SequenceAnnotationService<AACon>\r
  24                 implements\r
  25                         SequenceAnnotation<AACon> {\r
  26 \r
  27         private static Logger log = Logger.getLogger(AAConWS.class);\r
  28 \r
  29         public AAConWS() {\r
  30                 super(new AACon(), log);\r
  31         }\r
  32 \r
  33         /*\r
  34          * @SuppressWarnings("unchecked") public JalviewAnnotation\r
  35          * getJalviewAnnotation(String jobId) throws ResultNotAvailableException {\r
  36          * MultiAnnotatedSequence<Method> result = getResult(jobId); // TODO //\r
  37          * log(jobId, "getResults"); return result.toJalviewAnnotation(); }\r
  38          */\r
  39 \r
  40         @Override\r
  41         public String analize(List<FastaSequence> sequences)\r
  42                         throws UnsupportedRuntimeException, LimitExceededException,\r
  43                         JobSubmissionException {\r
  44                 WSUtil.validateAAConInput(sequences);\r
  45                 ConfiguredExecutable<AACon> confAAcon = init(sequences);\r
  46 \r
  47                 // set default conservation method to fastest - SHENKIN\r
  48                 // TODO: This violates encapsulation, should be moved to the runners\r
  49                 // level.\r
  50                 confAAcon.addParameters(Arrays.asList("-m=SHENKIN"));\r
  51                 return WSUtil.analize(sequences, confAAcon, log, "AAConWS analize",\r
  52                                 getLimit(""));\r
  53         }\r
  54 \r
  55         @Override\r
  56         public ChunkHolder pullExecStatistics(String jobId, long position) {\r
  57                 WSUtil.validateJobId(jobId);\r
  58                 String file = Configurator.getWorkDirectory(jobId) + File.separator\r
  59                                 + AACon.getStatFile();\r
  60                 return WSUtil.pullFile(file, position);\r
  61         }\r
  62 \r
  63 }\r