+package compbio.ws.server;\r
+\r
+import java.io.File;\r
+import java.util.List;\r
+\r
+import org.apache.log4j.Logger;\r
+\r
+import compbio.data.sequence.Alignment;\r
+import compbio.data.sequence.FastaSequence;\r
+import compbio.engine.AsyncExecutor;\r
+import compbio.engine.Configurator;\r
+import compbio.engine.client.ConfiguredExecutable;\r
+import compbio.engine.client.SkeletalExecutable;\r
+import compbio.metadata.ChunkHolder;\r
+import compbio.metadata.JobSubmissionException;\r
+import compbio.metadata.Limit;\r
+import compbio.metadata.Option;\r
+import compbio.metadata.Preset;\r
+import compbio.metadata.ResultNotAvailableException;\r
+import compbio.metadata.WrongParameterException;\r
+import compbio.runner.msa.ClustalW;\r
+\r
+/**\r
+ * \r
+ * TODO to complete after the approach is tested with SequenceAnnotation!\r
+ * \r
+ * Common methods for all SequenceAnnotation web services\r
+ * \r
+ * @author pvtroshin\r
+ * \r
+ * @param <T>\r
+ * \r
+ * @version 1.0 June 2011\r
+ * @since 2.0\r
+ */\r
+public abstract class _MsaService<T> extends GenericMetadataService {\r
+\r
+ /*\r
+ * FIXME - instances of the Runner (?) and their types should be defined in\r
+ * Executable IF\r
+ */\r
+ _MsaService(SkeletalExecutable<T> exec, Logger log) {\r
+ super(exec, log);\r
+ }\r
+\r
+ public String align(List<FastaSequence> sequences)\r
+ throws JobSubmissionException {\r
+\r
+ WSUtil.validateFastaInput(sequences);\r
+ ConfiguredExecutable<T> confClust = init(sequences);\r
+ return WSUtil.align(sequences, confClust, log, "align", getLimit(""));\r
+ }\r
+\r
+ public String presetAlign(List<FastaSequence> sequences, Preset<T> preset)\r
+ throws JobSubmissionException, WrongParameterException {\r
+ WSUtil.validateFastaInput(sequences);\r
+ if (preset == null) {\r
+ throw new WrongParameterException("Preset must be provided!");\r
+ }\r
+ Limit<T> limit = getLimit(preset.getName());\r
+ ConfiguredExecutable<T> confClust = init(sequences);\r
+ confClust.addParameters(preset.getOptions());\r
+ return WSUtil.align(sequences, confClust, log, "presetAlign", limit);\r
+ }\r
+\r
+ public String customAlign(List<FastaSequence> sequences,\r
+ List<Option<T>> options) throws JobSubmissionException,\r
+ WrongParameterException {\r
+ WSUtil.validateFastaInput(sequences);\r
+ ConfiguredExecutable<T> confClust = init(sequences);\r
+ List<String> params = WSUtil.getCommands(options,\r
+ ClustalW.KEY_VALUE_SEPARATOR);\r
+ confClust.addParameters(params);\r
+ log.info("Setting parameters: " + params);\r
+ return WSUtil.align(sequences, confClust, log, "customAlign",\r
+ getLimit(""));\r
+ }\r
+\r
+ @SuppressWarnings("unchecked")\r
+ public Alignment getResult(String jobId) throws ResultNotAvailableException {\r
+\r
+ WSUtil.validateJobId(jobId);\r
+ AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
+ ConfiguredExecutable<T> clustal = (ConfiguredExecutable<T>) asyncEngine\r
+ .getResults(jobId);\r
+ Alignment al = clustal.getResults();\r
+ return al;\r
+ }\r
+\r
+ @Override\r
+ public ChunkHolder pullExecStatistics(String jobId, long position) {\r
+ WSUtil.validateJobId(jobId);\r
+ String file = Configurator.getWorkDirectory(jobId) + File.separator\r
+ + ClustalW.getStatFile();\r
+ ChunkHolder cholder = WSUtil.pullFile(file, position);\r
+ return cholder;\r
+ }\r
+\r
+}\r