- // Hardcoded gapchar '-' in this method\r
- \r
- public static <T> String fold(Alignment alignment,\r
- ConfiguredExecutable<T> confExec, Logger logger,\r
- String callingMethod, Limit<T> limit)\r
- throws LimitExceededException, JobSubmissionException {\r
- \r
- List<FastaSequence> sequences = alignment.getSequences();\r
- if (limit != null && limit.isExceeded(sequences)) {\r
- throw LimitExceededException.newLimitExceeded(limit, sequences);\r
- }\r
- compbio.runner.Util.writeClustalInput(sequences, confExec, '-');\r
- System.out.println("WSUtil-fold: Writing the clustal input file on the server: to file: "\r
- + confExec.getInput());\r
- System.out.println("WSUtil-fold: The executable is configured with parameters: " \r
- + confExec.getParameters());\r
-// System.out.println("WSUTil-fold: Dump the configured executable:\n" \r
-// + confExec.toString());\r
- AsyncExecutor engine = Configurator.getAsyncEngine(confExec);\r
- String jobId = engine.submitJob(confExec);\r
- reportUsage(confExec, logger);\r
- return jobId;\r
- }\r