X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=webservices%2Fcompbio%2Fws%2Fserver%2FWSUtil.java;h=62996e521d709b0c67b26be0e1814ba382b97acc;hb=fab6bab770b548a0c99ed6f5dfb46f5aa99f67c7;hp=dd1051f7f6b823f8b5ea74c68c65cb99b79d9406;hpb=cb02e8a08893701386c270a8bf9d0f08b9cbc4db;p=jabaws.git

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