X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=webservices%2Fcompbio%2Fws%2Fserver%2FWSUtil.java;h=d0c92267353ecdeda930eb844e8f0494c591cb65;hb=5578f2d3e8226bd931755da3feeecb91fdb26c3f;hp=da4182c6b85b215a734bf2e7b0064e65e9677df9;hpb=0f73a668ad9aa4905b4c90948af0ede97b544c90;p=jabaws.git

diff --git a/webservices/compbio/ws/server/WSUtil.java b/webservices/compbio/ws/server/WSUtil.java
index da4182c..d0c9226 100644
--- a/webservices/compbio/ws/server/WSUtil.java
+++ b/webservices/compbio/ws/server/WSUtil.java
@@ -115,8 +115,7 @@ public final class WSUtil {
 
 	static <T> void reportUsage(ConfiguredExecutable<T> confExec, Logger logger) {
 		if (GAUtils.IS_GA_ENABLED) {
-			Services service = ServicesUtil.getServiceByRunner(confExec
-					.getExecutable().getClass());
+			Services service = ServicesUtil.getServiceByRunner(confExec.getExecutable().getClass());
 			GAUtils.reportUsage(service);
 			logger.info("Reporting GA usage for " + service);
 		}
@@ -128,15 +127,14 @@ public final class WSUtil {
 		if (limit != null && limit.isExceeded(sequences)) {
 			throw LimitExceededException.newLimitExceeded(limit, sequences);
 		}
-		log.debug("Method: " + method + " with task: " + confExec.getTaskId());
 		compbio.runner.Util.writeInput(sequences, confExec);
 		AsyncExecutor engine = Configurator.getAsyncEngine(confExec);
 		String jobId = engine.submitJob(confExec);
 		reportUsage(confExec, log);
 		return jobId;
 	}
-	
-	// Same as analize but Alifold takes clustal input not fasta
+
+	// Same as analize(...) but RNAalifold takes clustal input not fasta
 	// An if condition in the above method might be a better solution but 
 	// you need a way of finding out the type of confExec at runtime
 	
@@ -146,8 +144,6 @@ public final class WSUtil {
 		if (limit != null && limit.isExceeded(sequences)) {
 			throw LimitExceededException.newLimitExceeded(limit, sequences);
 		}
-		log.debug("Method: " + method + " with task: " + confExec.getTaskId());
-		// This line is different from the above method
 		compbio.runner.Util.writeClustalInput(sequences, confExec, '-');
 		AsyncExecutor engine = Configurator.getAsyncEngine(confExec);
 		String jobId = engine.submitJob(confExec);
@@ -178,10 +174,28 @@ public final class WSUtil {
 			}
 			if (fs.getLength() != len) {
 				throw new JobSubmissionException(
-						"All sequences must be of the same length. Please align "
-								+ "the sequences prior to submission! The first sequence length is : "
-								+ len + " but the sequence '" + fs.getId()
-								+ "' length is " + fs.getLength());
+						"All sequences must be of the same length. Please align the sequences " + 
+						" prior to submission! The first sequence length is : " + len + 
+						" but the sequence '" + fs.getId() + "' length is " + fs.getLength());
+			}
+		}
+	}
+
+	public static void validateJpredInput(List<FastaSequence> sequences)
+			throws JobSubmissionException {
+		validateFastaInput(sequences);
+		int len = 0;
+		for (FastaSequence fs : sequences) {
+			if (len == 0) {
+				len = fs.getLength();
+				continue;
+			}
+			if (fs.getLength() != len) {
+				System.out.println("FASTA rec: id = " + fs.getId() + ": seq = " + fs.getSequence());
+				throw new JobSubmissionException(
+						"All sequences must be of the same length. Please align the sequences " + 
+						" prior to submission! The first sequence length is : " + len + 
+						" but the sequence '" + fs.getId() + "' length is " + fs.getLength());
 			}
 		}
 	}
@@ -190,48 +204,10 @@ public final class WSUtil {
 			throws ResultNotAvailableException {
 		WSUtil.validateJobId(jobId);
 		AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);
-		ConfiguredExecutable<T> aacon = (ConfiguredExecutable<T>) asyncEngine
-				.getResults(jobId);
-		
+		ConfiguredExecutable<T> aacon = (ConfiguredExecutable<T>) asyncEngine.getResults(jobId);
 		ScoreManager mas = aacon.getResults();
-		
 		log.trace(jobId + " getConservation : " + mas);
 		return mas;
 	}
-	
 
-	/*
-	 * UNUSED
-	 * 
-	 * @SuppressWarnings("unchecked") static <T> LimitsManager<T>
-	 * getLimits(Class<? extends Executable<T>> clazz, WebServiceContext
-	 * wsContext) {
-	 * 
-	 * String LIMIT_KEY = CACHE_KEY + clazz.getCanonicalName(); LimitsManager<T>
-	 * limit = (LimitsManager<T>) getObjectFromApplContext( LIMIT_KEY,
-	 * wsContext); if (limit == null) { synchronized (WSUtil.class) { limit =
-	 * (LimitsManager<T>) getObjectFromApplContext(LIMIT_KEY, wsContext); if
-	 * (limit == null) { limit = compbio.runner.Util
-	 * .getLimits((Class<Executable<T>>) clazz);
-	 * addObjectToApplContext(wsContext, LIMIT_KEY, limit); } } } return limit;
-	 * }
-	 * 
-	 * static void addObjectToApplContext(WebServiceContext wsContext, String
-	 * objKey, Object obj) { assert !Util.isEmpty(objKey) :
-	 * "Key for the object must not be empty! "; assert wsContext != null;
-	 * 
-	 * ServletContext ctx = ((javax.servlet.ServletContext) wsContext
-	 * .getMessageContext().get(MessageContext. SERVLET_CONTEXT)); assert ctx !=
-	 * null; log.debug("Adding object with key '" + objKey + "' and value '" +
-	 * obj + "' to the application context"); ctx.setAttribute(objKey, obj); }
-	 * static Object getObjectFromApplContext(String objKey, WebServiceContext
-	 * wsContext) { assert !Util.isEmpty(objKey) :
-	 * "Key for the object must not be empty! "; assert wsContext != null;
-	 * 
-	 * ServletContext ctx = ((javax.servlet.ServletContext) wsContext
-	 * .getMessageContext().get(MessageContext. SERVLET_CONTEXT)); Object obj =
-	 * ctx.getAttribute(objKey); log.trace("Retrieving object with key '" +
-	 * objKey + "' and value '" + obj + "' from the application context");
-	 * return obj; }
-	 */
 }