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.SequenceAnnotation;\r
  12 import compbio.data.sequence.FastaSequence;\r
  13 import compbio.engine.Configurator;\r
  14 import compbio.engine.client.ConfiguredExecutable;\r
  15 import compbio.metadata.ChunkHolder;\r
  16 import compbio.metadata.JobSubmissionException;\r
  17 import compbio.metadata.LimitExceededException;\r
  18 import compbio.metadata.UnsupportedRuntimeException;\r
  19 import compbio.runner.conservation.AACon;\r
  20 \r
  21 @WebService(endpointInterface = "compbio.data.msa.SequenceAnnotation", targetNamespace = "http://msa.data.compbio/01/12/2010/", serviceName = "AAConWS")\r
  22 public class AAConWS extends SequenceAnnotationService<AACon>\r
  23                 implements\r
  24                         SequenceAnnotation<AACon> {\r
  25 \r
  26         private static Logger log = Logger.getLogger(AAConWS.class);\r
  27 \r
  28         public AAConWS() {\r
  29                 super(new AACon(), log);\r
  30         }\r
  31 \r
  32         /*\r
  33          * @SuppressWarnings("unchecked") public JalviewAnnotation\r
  34          * getJalviewAnnotation(String jobId) throws ResultNotAvailableException {\r
  35          * MultiAnnotatedSequence<Method> result = getResult(jobId); // TODO //\r
  36          * log(jobId, "getResults"); return result.toJalviewAnnotation(); }\r
  37          */\r
  38 \r
  39         @Override\r
  40         public String analize(List<FastaSequence> sequences)\r
  41                         throws UnsupportedRuntimeException, LimitExceededException,\r
  42                         JobSubmissionException {\r
  43                 WSUtil.validateAAConInput(sequences);\r
  44                 ConfiguredExecutable<AACon> confAAcon = init(sequences);\r
  45 \r
  46                 // set default conservation method to fastest - SHENKIN\r
  47                 // TODO: This violates encapsulation, should be moved to the runners\r
  48                 // level.\r
  49                 confAAcon.addParameters(Arrays.asList("-m=SHENKIN"));\r
  50                 return WSUtil.analize(sequences, confAAcon, log, "AAConWS analize",\r
  51                                 getLimit(""));\r
  52         }\r
  53 \r
  54         @Override\r
  55         public ChunkHolder pullExecStatistics(String jobId, long position) {\r
  56                 WSUtil.validateJobId(jobId);\r
  57                 String file = Configurator.getWorkDirectory(jobId) + File.separator\r
  58                                 + AACon.getStatFile();\r
  59                 return WSUtil.pullFile(file, position);\r
  60         }\r
  61 \r
  62 }\r