Merge branch 'JABAWS_Release_2_0'

[jabaws.git] / webservices / compbio / ws / server / _MsaService.java

diff --git a/webservices/compbio/ws/server/_MsaService.java b/webservices/compbio/ws/server/_MsaService.java
deleted file mode 100644 (file)
index f967f61..0000000
--- a/webservices/compbio/ws/server/_MsaService.java
+++ /dev/null
@@ -1,116 +0,0 @@
-/* Copyright (c) 2011 Peter Troshin\r
- *  \r
- *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0     \r
- * \r
- *  This library is free software; you can redistribute it and/or modify it under the terms of the\r
- *  Apache License version 2 as published by the Apache Software Foundation\r
- * \r
- *  This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
- *  even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
- *  License for more details.\r
- * \r
- *  A copy of the license is in apache_license.txt. It is also available here:\r
- * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
- * \r
- * Any republication or derived work distributed in source code form\r
- * must include this copyright and license notice.\r
- */\r
-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