throws JobSubmissionException {\r
WSUtil.validateFastaInput(sequences);\r
ConfiguredExecutable<Muscle> confMuscle = init(sequences);\r
throws JobSubmissionException {\r
WSUtil.validateFastaInput(sequences);\r
ConfiguredExecutable<Muscle> confMuscle = init(sequences);\r
- return WSUtil.align(sequences, confMuscle, null, "align", getLimit(""));\r
+ return WSUtil.align(sequences, confMuscle, log, "align", getLimit(""));\r
List<String> params = WSUtil.getCommands(options,\r
Muscle.KEY_VALUE_SEPARATOR);\r
confMuscle.addParameters(params);\r
List<String> params = WSUtil.getCommands(options,\r
Muscle.KEY_VALUE_SEPARATOR);\r
confMuscle.addParameters(params);\r
- return WSUtil.align(sequences, confMuscle, null, "customAlign",\r
+ return WSUtil.align(sequences, confMuscle, log, "customAlign",\r
ConfiguredExecutable<Muscle> confMuscle = init(sequences);\r
confMuscle.addParameters(preset.getOptions());\r
Limit<Muscle> limit = getLimit(preset.getName());\r
ConfiguredExecutable<Muscle> confMuscle = init(sequences);\r
confMuscle.addParameters(preset.getOptions());\r
Limit<Muscle> limit = getLimit(preset.getName());\r
- return WSUtil.align(sequences, confMuscle, null, "presetAlign", limit);\r
+ return WSUtil.align(sequences, confMuscle, log, "presetAlign", limit);\r