- @Override\r
- public boolean cancelJob(String jobId) {\r
- WSUtil.validateJobId(jobId);\r
- return WSUtil.cancelJob(jobId);\r
- }\r
-\r
- @Override\r
- public JobStatus getJobStatus(String jobId) {\r
- WSUtil.validateJobId(jobId);\r
- return WSUtil.getJobStatus(jobId);\r
- }\r
-\r
- @Override\r
- public PresetManager<Jronn> getPresets() {\r
- return jronnPresets;\r
- }\r
-\r
- @Override\r
- public RunnerConfig<Jronn> getRunnerOptions() {\r
- return jronnOptions;\r
- }\r
-\r
- String analize(List<FastaSequence> sequences,\r
- ConfiguredExecutable<Jronn> confExec, Logger log, String method,\r
- Limit<Jronn> limit) throws JobSubmissionException {\r
- if (limit != null && limit.isExceeded(sequences)) {\r
- throw LimitExceededException.newLimitExceeded(limit, sequences);\r
- }\r
-\r
- compbio.runner.Util.writeInput(sequences, confExec);\r
- AsyncExecutor engine = Configurator.getAsyncEngine(confExec);\r
- String jobId = engine.submitJob(confExec);\r
- return jobId;\r
- }\r
-\r
- @Override\r
- public String analize(List<FastaSequence> sequences)\r
- throws UnsupportedRuntimeException, LimitExceededException,\r
- JobSubmissionException {\r
- WSUtil.validateFastaInput(sequences);\r
- ConfiguredExecutable<Jronn> confJronn = init(sequences);\r
-\r
- return analize(sequences, confJronn, null, "analize", getLimit(""));\r
- }\r
-\r
- @Override\r
- public String customAnalize(List<FastaSequence> sequences,\r
- List<Option<Jronn>> options) throws UnsupportedRuntimeException,\r
- LimitExceededException, JobSubmissionException,\r
- WrongParameterException {\r
- WSUtil.validateFastaInput(sequences);\r
- ConfiguredExecutable<Jronn> confJronn = init(sequences);\r
-\r
- List<String> params = WSUtil.getCommands(options,\r
- AACon.KEY_VALUE_SEPARATOR);\r
- confJronn.addParameters(params);\r
- return analize(sequences, confJronn, null, "customAnalize",\r
- getLimit(""));\r
- }\r
-\r
- @Override\r
- public String presetAnalize(List<FastaSequence> sequences,\r
- Preset<Jronn> preset) throws UnsupportedRuntimeException,\r
- LimitExceededException, JobSubmissionException,\r
- WrongParameterException {\r
- WSUtil.validateFastaInput(sequences);\r
- if (preset == null) {\r
- throw new WrongParameterException("Preset must be provided!");\r
- }\r
- ConfiguredExecutable<Jronn> confJronn = init(sequences);\r
- confJronn.addParameters(preset.getOptions());\r
- Limit<Jronn> limit = getLimit(preset.getName());\r
- return WSUtil.align(sequences, confJronn, null, "presetAnalize", limit);\r
- }\r
-\r