webservices/compbio/ws/server/_MsaService.java

   1 /* Copyright (c) 2011 Peter Troshin\r
   2  *  \r
   3  *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0     \r
   4  * \r
   5  *  This library is free software; you can redistribute it and/or modify it under the terms of the\r
   6  *  Apache License version 2 as published by the Apache Software Foundation\r
   7  * \r
   8  *  This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
   9  *  even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
  10  *  License for more details.\r
  11  * \r
  12  *  A copy of the license is in apache_license.txt. It is also available here:\r
  13  * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
  14  * \r
  15  * Any republication or derived work distributed in source code form\r
  16  * must include this copyright and license notice.\r
  17  */\r
  18 package compbio.ws.server;\r
  19 \r
  20 import java.io.File;\r
  21 import java.util.List;\r
  22 \r
  23 import org.apache.log4j.Logger;\r
  24 \r
  25 import compbio.data.sequence.Alignment;\r
  26 import compbio.data.sequence.FastaSequence;\r
  27 import compbio.engine.AsyncExecutor;\r
  28 import compbio.engine.Configurator;\r
  29 import compbio.engine.client.ConfiguredExecutable;\r
  30 import compbio.engine.client.SkeletalExecutable;\r
  31 import compbio.metadata.ChunkHolder;\r
  32 import compbio.metadata.JobSubmissionException;\r
  33 import compbio.metadata.Limit;\r
  34 import compbio.metadata.Option;\r
  35 import compbio.metadata.Preset;\r
  36 import compbio.metadata.ResultNotAvailableException;\r
  37 import compbio.metadata.WrongParameterException;\r
  38 import compbio.runner.msa.ClustalW;\r
  39 \r
  40 /**\r
  41  * \r
  42  * TODO to complete after the approach is tested with SequenceAnnotation!\r
  43  * \r
  44  * Common methods for all SequenceAnnotation web services\r
  45  * \r
  46  * @author pvtroshin\r
  47  * \r
  48  * @param <T>\r
  49  * \r
  50  * @version 1.0 June 2011\r
  51  * @since 2.0\r
  52  */\r
  53 public abstract class _MsaService<T> extends GenericMetadataService {\r
  54 \r
  55         /*\r
  56          * FIXME - instances of the Runner (?) and their types should be defined in\r
  57          * Executable IF\r
  58          */\r
  59         _MsaService(SkeletalExecutable<T> exec, Logger log) {\r
  60                 super(exec, log);\r
  61         }\r
  62 \r
  63         public String align(List<FastaSequence> sequences)\r
  64                         throws JobSubmissionException {\r
  65 \r
  66                 WSUtil.validateFastaInput(sequences);\r
  67                 ConfiguredExecutable<T> confClust = init(sequences);\r
  68                 return WSUtil.align(sequences, confClust, log, "align", getLimit(""));\r
  69         }\r
  70 \r
  71         public String presetAlign(List<FastaSequence> sequences, Preset<T> preset)\r
  72                         throws JobSubmissionException, WrongParameterException {\r
  73                 WSUtil.validateFastaInput(sequences);\r
  74                 if (preset == null) {\r
  75                         throw new WrongParameterException("Preset must be provided!");\r
  76                 }\r
  77                 Limit<T> limit = getLimit(preset.getName());\r
  78                 ConfiguredExecutable<T> confClust = init(sequences);\r
  79                 confClust.addParameters(preset.getOptions());\r
  80                 return WSUtil.align(sequences, confClust, log, "presetAlign", limit);\r
  81         }\r
  82 \r
  83         public String customAlign(List<FastaSequence> sequences,\r
  84                         List<Option<T>> options) throws JobSubmissionException,\r
  85                         WrongParameterException {\r
  86                 WSUtil.validateFastaInput(sequences);\r
  87                 ConfiguredExecutable<T> confClust = init(sequences);\r
  88                 List<String> params = WSUtil.getCommands(options,\r
  89                                 ClustalW.KEY_VALUE_SEPARATOR);\r
  90                 confClust.addParameters(params);\r
  91                 log.info("Setting parameters: " + params);\r
  92                 return WSUtil.align(sequences, confClust, log, "customAlign",\r
  93                                 getLimit(""));\r
  94         }\r
  95 \r
  96         @SuppressWarnings("unchecked")\r
  97         public Alignment getResult(String jobId) throws ResultNotAvailableException {\r
  98 \r
  99                 WSUtil.validateJobId(jobId);\r
 100                 AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
 101                 ConfiguredExecutable<T> clustal = (ConfiguredExecutable<T>) asyncEngine\r
 102                                 .getResults(jobId);\r
 103                 Alignment al = clustal.getResults();\r
 104                 return al;\r
 105         }\r
 106 \r
 107         @Override\r
 108         public ChunkHolder pullExecStatistics(String jobId, long position) {\r
 109                 WSUtil.validateJobId(jobId);\r
 110                 String file = Configurator.getWorkDirectory(jobId) + File.separator\r
 111                                 + ClustalW.getStatFile();\r
 112                 ChunkHolder cholder = WSUtil.pullFile(file, position);\r
 113                 return cholder;\r
 114         }\r
 115 \r
 116 }\r