-/* Copyright (c) 2009 Peter Troshin\r
+/* Copyright (c) 2011 Peter Troshin\r
* \r
- * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0\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
import org.apache.log4j.Logger;\r
\r
+import compbio.data.msa.JABAService;\r
import compbio.data.msa.MsaWS;\r
import compbio.data.sequence.Alignment;\r
import compbio.data.sequence.FastaSequence;\r
+import compbio.data.sequence.Program;\r
import compbio.engine.AsyncExecutor;\r
import compbio.engine.Configurator;\r
import compbio.engine.client.ConfiguredExecutable;\r
import compbio.runner.Util;\r
import compbio.runner.msa.Tcoffee;\r
\r
-@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = "http://msa.data.compbio/01/01/2010/", serviceName = "TcoffeeWS")\r
+@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = JABAService.SERVICE_NAMESPACE, serviceName = "TcoffeeWS")\r
public class TcoffeeWS implements MsaWS<Tcoffee> {\r
\r
private static Logger log = Logger.getLogger(TcoffeeWS.class);\r
\r
- private static final RunnerConfig<Tcoffee> tcoffeeOptions = Util\r
- .getSupportedOptions(Tcoffee.class);\r
+ private static final RunnerConfig<Tcoffee> tcoffeeOptions = Util.getSupportedOptions(Tcoffee.class);\r
\r
- private static final PresetManager<Tcoffee> tcoffeePresets = Util\r
- .getPresets(Tcoffee.class);\r
+ private static final PresetManager<Tcoffee> tcoffeePresets = Util.getPresets(Tcoffee.class);\r
\r
- private static final LimitsManager<Tcoffee> limitMan = compbio.engine.client.Util\r
- .getLimits(new Tcoffee().getType());\r
+ private static final LimitsManager<Tcoffee> limitMan = compbio.engine.client.Util.getLimits(new Tcoffee().getType());\r
\r
@Override\r
public String align(List<FastaSequence> sequences)\r
throws JobSubmissionException {\r
WSUtil.validateFastaInput(sequences);\r
ConfiguredExecutable<Tcoffee> confTcoffee = init(sequences);\r
- return WSUtil\r
- .align(sequences, confTcoffee, null, "align", getLimit(""));\r
+ return WSUtil.align(sequences, confTcoffee, log, "align", getLimit(""));\r
}\r
\r
ConfiguredExecutable<Tcoffee> init(List<FastaSequence> sequences)\r
\r
WSUtil.validateFastaInput(sequences);\r
ConfiguredExecutable<Tcoffee> confTcoffee = init(sequences);\r
- List<String> params = WSUtil.getCommands(options,\r
- Tcoffee.KEY_VALUE_SEPARATOR);\r
+ List<String> params = WSUtil.getCommands(options, Tcoffee.KEY_VALUE_SEPARATOR);\r
log.info("Setting parameters:" + params);\r
confTcoffee.addParameters(params);\r
- return WSUtil.align(sequences, confTcoffee, null, "customAlign",\r
- getLimit(""));\r
+ return WSUtil.align(sequences, confTcoffee, log, "customAlign", getLimit(""));\r
}\r
\r
@Override\r
ConfiguredExecutable<Tcoffee> confTcoffee = init(sequences);\r
confTcoffee.addParameters(preset.getOptions());\r
Limit<Tcoffee> limit = getLimit(preset.getName());\r
- return WSUtil.align(sequences, confTcoffee, null, "presetAlign", limit);\r
+ return WSUtil.align(sequences, confTcoffee, log, "presetAlign", limit);\r
}\r
\r
@SuppressWarnings("unchecked")\r
ConfiguredExecutable<Tcoffee> tcoffee = (ConfiguredExecutable<Tcoffee>) asyncEngine\r
.getResults(jobId);\r
Alignment al = tcoffee.getResults();\r
- // log(jobId, "getResults");\r
- return al;\r
+ return new Alignment (al.getSequences(), Program.Tcoffee, '-');\r
}\r
\r
@Override\r