return jobId;\r
}\r
\r
- // Hardcoded gapchar '-'\r
- \r
- public static <T> String fold(List<FastaSequence> sequences,\r
- ConfiguredExecutable<T> confExec, Logger logger,\r
- String callingMethod, Limit<T> limit)\r
- throws LimitExceededException, JobSubmissionException {\r
- \r
- if (limit != null && limit.isExceeded(sequences)) {\r
- throw LimitExceededException.newLimitExceeded(limit, sequences);\r
- }\r
- compbio.runner.Util.writeClustalInput(sequences, confExec, '-');\r
- AsyncExecutor engine = Configurator.getAsyncEngine(confExec);\r
- String jobId = engine.submitJob(confExec);\r
- reportUsage(confExec, logger);\r
- return jobId;\r
- }\r
\r
static <T> void reportUsage(ConfiguredExecutable<T> confExec, Logger logger) {\r
if (GAUtils.IS_GA_ENABLED) {\r
throw LimitExceededException.newLimitExceeded(limit, sequences);\r
}\r
log.debug("Method: " + method + " with task: " + confExec.getTaskId());\r
-\r
compbio.runner.Util.writeInput(sequences, confExec);\r
AsyncExecutor engine = Configurator.getAsyncEngine(confExec);\r
String jobId = engine.submitJob(confExec);\r
reportUsage(confExec, log);\r
return jobId;\r
}\r
+ \r
+ // Same as analize but Alifold takes clustal input not fasta\r
+ // An if condition in the above method might be a better solution but \r
+ // you need a way of finding out the type of confExec at runtime\r
+ \r
+ public static <T> String fold(List<FastaSequence> sequences,\r
+ ConfiguredExecutable<T> confExec, Logger log, String method,\r
+ Limit<T> limit) throws JobSubmissionException {\r
+ if (limit != null && limit.isExceeded(sequences)) {\r
+ throw LimitExceededException.newLimitExceeded(limit, sequences);\r
+ }\r
+ log.debug("Method: " + method + " with task: " + confExec.getTaskId());\r
+ // This line is different from the above method\r
+ compbio.runner.Util.writeClustalInput(sequences, confExec, '-');\r
+ AsyncExecutor engine = Configurator.getAsyncEngine(confExec);\r
+ String jobId = engine.submitJob(confExec);\r
+ reportUsage(confExec, log);\r
+ return jobId;\r
+ }\r
\r
/*\r
* TODO Rewrite using purely CommandBuilder. This is breaking encapsulation\r
}\r
if (fs.getLength() != len) {\r
throw new JobSubmissionException(\r
- "All sequences must be of the same length. Please align "\r
- + "the sequences prior to submission! The first sequence length is : "\r
- + len + " but the sequence '" + fs.getId()\r
- + "' length is " + fs.getLength());\r
+ "All sequences must be of the same length. Please align the sequences " + \r
+ " prior to submission! The first sequence length is : " + len + \r
+ " but the sequence '" + fs.getId() + "' length is " + fs.getLength());\r
+ }\r
+ }\r
+ }\r
+\r
+ public static void validateJpredInput(List<FastaSequence> sequences)\r
+ throws JobSubmissionException {\r
+ validateFastaInput(sequences);\r
+ int len = 0;\r
+ for (FastaSequence fs : sequences) {\r
+ if (len == 0) {\r
+ len = fs.getLength();\r
+ continue;\r
+ }\r
+ if (fs.getLength() != len) {\r
+ System.out.println("FASTA rec: id = " + fs.getId() + ": seq = " + fs.getSequence());\r
+ throw new JobSubmissionException(\r
+ "All sequences must be of the same length. Please align the sequences " + \r
+ " prior to submission! The first sequence length is : " + len + \r
+ " but the sequence '" + fs.getId() + "' length is " + fs.getLength());\r
}\r
}\r
}\r
throws ResultNotAvailableException {\r
WSUtil.validateJobId(jobId);\r
AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
- ConfiguredExecutable<T> aacon = (ConfiguredExecutable<T>) asyncEngine\r
- .getResults(jobId);\r
+ ConfiguredExecutable<T> aacon = (ConfiguredExecutable<T>) asyncEngine.getResults(jobId);\r
ScoreManager mas = aacon.getResults();\r
+ \r
log.trace(jobId + " getConservation : " + mas);\r
return mas;\r
}\r
+ \r
\r
/*\r
* UNUSED\r