webservices/compbio/ws/server/_MsaService.java

   1 package compbio.ws.server;\r
   2 \r
   3 import java.io.File;\r
   4 import java.util.List;\r
   5 \r
   6 import org.apache.log4j.Logger;\r
   7 \r
   8 import compbio.data.sequence.Alignment;\r
   9 import compbio.data.sequence.FastaSequence;\r
  10 import compbio.engine.AsyncExecutor;\r
  11 import compbio.engine.Configurator;\r
  12 import compbio.engine.client.ConfiguredExecutable;\r
  13 import compbio.engine.client.SkeletalExecutable;\r
  14 import compbio.metadata.ChunkHolder;\r
  15 import compbio.metadata.JobSubmissionException;\r
  16 import compbio.metadata.Limit;\r
  17 import compbio.metadata.Option;\r
  18 import compbio.metadata.Preset;\r
  19 import compbio.metadata.ResultNotAvailableException;\r
  20 import compbio.metadata.WrongParameterException;\r
  21 import compbio.runner.msa.ClustalW;\r
  22 \r
  23 /**\r
  24  * \r
  25  * TODO to complete after the approach is tested with SequenceAnnotation!\r
  26  * \r
  27  * Common methods for all SequenceAnnotation web services\r
  28  * \r
  29  * @author pvtroshin\r
  30  * \r
  31  * @param <T>\r
  32  * \r
  33  * @version 1.0 June 2011\r
  34  * @since 2.0\r
  35  */\r
  36 public abstract class _MsaService<T> extends GenericMetadataService {\r
  37 \r
  38         /*\r
  39          * FIXME - instances of the Runner (?) and their types should be defined in\r
  40          * Executable IF\r
  41          */\r
  42         _MsaService(SkeletalExecutable<T> exec, Logger log) {\r
  43                 super(exec, log);\r
  44         }\r
  45 \r
  46         public String align(List<FastaSequence> sequences)\r
  47                         throws JobSubmissionException {\r
  48 \r
  49                 WSUtil.validateFastaInput(sequences);\r
  50                 ConfiguredExecutable<T> confClust = init(sequences);\r
  51                 return WSUtil.align(sequences, confClust, log, "align", getLimit(""));\r
  52         }\r
  53 \r
  54         public String presetAlign(List<FastaSequence> sequences, Preset<T> preset)\r
  55                         throws JobSubmissionException, WrongParameterException {\r
  56                 WSUtil.validateFastaInput(sequences);\r
  57                 if (preset == null) {\r
  58                         throw new WrongParameterException("Preset must be provided!");\r
  59                 }\r
  60                 Limit<T> limit = getLimit(preset.getName());\r
  61                 ConfiguredExecutable<T> confClust = init(sequences);\r
  62                 confClust.addParameters(preset.getOptions());\r
  63                 return WSUtil.align(sequences, confClust, log, "presetAlign", limit);\r
  64         }\r
  65 \r
  66         public String customAlign(List<FastaSequence> sequences,\r
  67                         List<Option<T>> options) throws JobSubmissionException,\r
  68                         WrongParameterException {\r
  69                 WSUtil.validateFastaInput(sequences);\r
  70                 ConfiguredExecutable<T> confClust = init(sequences);\r
  71                 List<String> params = WSUtil.getCommands(options,\r
  72                                 ClustalW.KEY_VALUE_SEPARATOR);\r
  73                 confClust.addParameters(params);\r
  74                 log.info("Setting parameters: " + params);\r
  75                 return WSUtil.align(sequences, confClust, log, "customAlign",\r
  76                                 getLimit(""));\r
  77         }\r
  78 \r
  79         @SuppressWarnings("unchecked")\r
  80         public Alignment getResult(String jobId) throws ResultNotAvailableException {\r
  81 \r
  82                 WSUtil.validateJobId(jobId);\r
  83                 AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
  84                 ConfiguredExecutable<T> clustal = (ConfiguredExecutable<T>) asyncEngine\r
  85                                 .getResults(jobId);\r
  86                 Alignment al = clustal.getResults();\r
  87                 return al;\r
  88         }\r
  89 \r
  90         @Override\r
  91         public ChunkHolder pullExecStatistics(String jobId, long position) {\r
  92                 WSUtil.validateJobId(jobId);\r
  93                 String file = Configurator.getWorkDirectory(jobId) + File.separator\r
  94                                 + ClustalW.getStatFile();\r
  95                 ChunkHolder cholder = WSUtil.pullFile(file, position);\r
  96                 return cholder;\r
  97         }\r
  98 \r
  99 }\r