-/* 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
throws JobSubmissionException {\r
WSUtil.validateFastaInput(sequences);\r
ConfiguredExecutable<Probcons> confProbcons = init(sequences);\r
- return WSUtil.align(sequences, confProbcons, null, "align",\r
- getLimit(""));\r
+ return WSUtil\r
+ .align(sequences, confProbcons, log, "align", getLimit(""));\r
}\r
\r
ConfiguredExecutable<Probcons> init(List<FastaSequence> dataSet)\r
Probcons.KEY_VALUE_SEPARATOR);\r
log.info("Setting parameters:" + params);\r
confProbcons.addParameters(params);\r
- return WSUtil.align(sequences, confProbcons, null, "customAlign",\r
+ return WSUtil.align(sequences, confProbcons, log, "customAlign",\r
getLimit(""));\r
}\r
\r
ConfiguredExecutable<Probcons> confProbcons = init(sequences);\r
confProbcons.addParameters(preset.getOptions());\r
Limit<Probcons> limit = getLimit(preset.getName());\r
- return WSUtil\r
- .align(sequences, confProbcons, null, "presetAlign", limit);\r
+ return WSUtil.align(sequences, confProbcons, log, "presetAlign", limit);\r
}\r
\r
@SuppressWarnings("unchecked")\r