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
Tcoffee.KEY_VALUE_SEPARATOR);\r
log.info("Setting parameters:" + params);\r
confTcoffee.addParameters(params);\r
- return WSUtil.align(sequences, confTcoffee, null, "customAlign",\r
+ return WSUtil.align(sequences, confTcoffee, log, "customAlign",\r
getLimit(""));\r
}\r
\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