Adding AAConWS

[jabaws.git] / webservices / compbio / ws / server / WSUtil.java

diff --git a/webservices/compbio/ws/server/WSUtil.java b/webservices/compbio/ws/server/WSUtil.java
index dd1051f..62996e5 100644 (file)
--- a/webservices/compbio/ws/server/WSUtil.java
+++ b/webservices/compbio/ws/server/WSUtil.java
@@ -36,73 +36,73 @@ import compbio.util.Timer;
 \r
 public final class WSUtil {\r
 \r
-    public static final void validateJobId(String jobId)\r
-           throws InvalidParameterException {\r
-       if (!compbio.engine.client.Util.isValidJobId(jobId)) {\r
-           throw new InvalidParameterException(\r
-                   "JobId is not provided or cannot be recognised! Given value: "\r
-                           + jobId);\r
+       public static final void validateJobId(String jobId)\r
+                       throws InvalidParameterException {\r
+               if (!compbio.engine.client.Util.isValidJobId(jobId)) {\r
+                       throw new InvalidParameterException(\r
+                                       "JobId is not provided or cannot be recognised! Given value: "\r
+                                                       + jobId);\r
+               }\r
        }\r
-    }\r
 \r
-    public static final void validateFastaInput(List<FastaSequence> sequences)\r
-           throws InvalidParameterException {\r
-       if (sequences == null || sequences.isEmpty()) {\r
-           throw new InvalidParameterException(\r
-                   "List of fasta sequences required but not provided! ");\r
+       public static final void validateFastaInput(List<FastaSequence> sequences)\r
+                       throws InvalidParameterException {\r
+               if (sequences == null || sequences.isEmpty()) {\r
+                       throw new InvalidParameterException(\r
+                                       "List of fasta sequences required but not provided! ");\r
+               }\r
        }\r
-    }\r
 \r
-    public static JobStatus getJobStatus(String jobId) {\r
-       AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
-       return asyncEngine.getJobStatus(jobId);\r
-    }\r
-\r
-    public static ChunkHolder pullFile(String file, long position) {\r
-       return ProgressGetter.pull(file, position);\r
-    }\r
+       public static JobStatus getJobStatus(String jobId) {\r
+               AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
+               return asyncEngine.getJobStatus(jobId);\r
+       }\r
 \r
-    public static byte getProgress(String jobId) {\r
-       throw new UnsupportedOperationException();\r
-    }\r
+       public static ChunkHolder pullFile(String file, long position) {\r
+               return ProgressGetter.pull(file, position);\r
+       }\r
 \r
-    public static AsyncExecutor getEngine(ConfiguredExecutable<?> confClustal) {\r
-       assert confClustal != null;\r
-       return Configurator.getAsyncEngine(confClustal);\r
-    }\r
+       public static byte getProgress(String jobId) {\r
+               throw new UnsupportedOperationException();\r
+       }\r
 \r
-    public static boolean cancelJob(String jobId) {\r
-       AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
-       return asyncEngine.cancelJob(jobId);\r
-    }\r
+       public static AsyncExecutor getEngine(ConfiguredExecutable<?> confClustal) {\r
+               assert confClustal != null;\r
+               return Configurator.getAsyncEngine(confClustal);\r
+       }\r
 \r
-    public static <T> String align(List<FastaSequence> sequences,\r
-           ConfiguredExecutable<T> confExec, WSLogger logger,\r
-           String callingMethod, Limit<T> limit)\r
-           throws LimitExceededException, JobSubmissionException {\r
-       Timer timer = Timer.getMilliSecondsTimer();\r
-       if (limit.isExceeded(sequences)) {\r
-           throw LimitExceededException.newLimitExceeded(limit, sequences);\r
+       public static boolean cancelJob(String jobId) {\r
+               AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
+               return asyncEngine.cancelJob(jobId);\r
        }\r
-       compbio.runner.Util.writeInput(sequences, confExec);\r
-       AsyncExecutor engine = Configurator.getAsyncEngine(confExec);\r
-       String jobId = engine.submitJob(confExec);\r
-       if (logger != null) {\r
-           logger.log(timer, callingMethod, jobId);\r
+\r
+       public static <T> String align(List<FastaSequence> sequences,\r
+                       ConfiguredExecutable<T> confExec, WSLogger logger,\r
+                       String callingMethod, Limit<T> limit)\r
+                       throws LimitExceededException, JobSubmissionException {\r
+               Timer timer = Timer.getMilliSecondsTimer();\r
+               if (limit != null && limit.isExceeded(sequences)) {\r
+                       throw LimitExceededException.newLimitExceeded(limit, sequences);\r
+               }\r
+               compbio.runner.Util.writeInput(sequences, confExec);\r
+               AsyncExecutor engine = Configurator.getAsyncEngine(confExec);\r
+               String jobId = engine.submitJob(confExec);\r
+               if (logger != null) {\r
+                       logger.log(timer, callingMethod, jobId);\r
+               }\r
+               return jobId;\r
        }\r
-       return jobId;\r
-    }\r
 \r
-    /*\r
-     * TODO Rewrite using purely CommandBuilder. This is breaking encapsulation\r
-     */\r
-    public static final <T> List<String> getCommands(List<Option<T>> options,\r
-           String keyValueSeparator) {\r
-       List<String> oList = new ArrayList<String>();\r
-       for (Option<T> o : options) {\r
-           oList.add(o.toCommand(keyValueSeparator));\r
+       /*\r
+        * TODO Rewrite using purely CommandBuilder. This is breaking encapsulation\r
+        */\r
+       public static final <T> List<String> getCommands(List<Option<T>> options,\r
+                       String keyValueSeparator) {\r
+               List<String> oList = new ArrayList<String>();\r
+               for (Option<T> o : options) {\r
+                       oList.add(o.toCommand(keyValueSeparator));\r
+               }\r
+               return oList;\r
        }\r
-       return oList;\r
-    }\r
 \r
 }\r