From: Daniel Barton <daluke.barton@gmail.com>
Date: Wed, 21 Aug 2013 10:55:21 +0000 (+0100)
Subject: Update the last commit which missed some files. RNAStructScoreManager
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=78cd52a6b64a7a0133b5467f80213f2d173f43f4;p=jabaws.git

Update the last commit which missed some files. RNAStructScoreManager
replacing RNAStruct. Webservices returns ScoreManager!?!-
---

diff --git a/webservices/compbio/ws/server/WSUtil.java b/webservices/compbio/ws/server/WSUtil.java
index 7646747..a3f96d8 100644
--- a/webservices/compbio/ws/server/WSUtil.java
+++ b/webservices/compbio/ws/server/WSUtil.java
@@ -27,6 +27,7 @@ import org.apache.log4j.Logger;
 
 import compbio.data.sequence.Alignment;
 import compbio.data.sequence.FastaSequence;
+import compbio.data.sequence.RNAStructScoreManager;
 import compbio.data.sequence.ScoreManager;
 import compbio.engine.AsyncExecutor;
 import compbio.engine.Configurator;
@@ -115,27 +116,27 @@ public final class WSUtil {
 	
 	// Hardcoded gapchar '-' in this method
 	
-	public static <T> String fold(Alignment alignment,
-			ConfiguredExecutable<T> confExec, Logger logger,
-			String callingMethod, Limit<T> limit)
-			throws LimitExceededException, JobSubmissionException {
-		
-		List<FastaSequence> sequences = alignment.getSequences();
-		if (limit != null && limit.isExceeded(sequences)) {
-			throw LimitExceededException.newLimitExceeded(limit, sequences);
-		}
-		compbio.runner.Util.writeClustalInput(sequences, confExec, '-');
-		System.out.println("WSUtil-fold: Writing the clustal input file on the server: to file: "
-				+ confExec.getInput());
-		System.out.println("WSUtil-fold: The executable is configured with parameters: " 
-				+ confExec.getParameters());
-//		System.out.println("WSUTil-fold: Dump the configured executable:\n" 
-//				+ confExec.toString());
-		AsyncExecutor engine = Configurator.getAsyncEngine(confExec);
-		String jobId = engine.submitJob(confExec);
-		reportUsage(confExec, logger);
-		return jobId;
-	}
+//	public static <T> String fold(Alignment alignment,
+//			ConfiguredExecutable<T> confExec, Logger logger,
+//			String callingMethod, Limit<T> limit)
+//			throws LimitExceededException, JobSubmissionException {
+//		
+//		List<FastaSequence> sequences = alignment.getSequences();
+//		if (limit != null && limit.isExceeded(sequences)) {
+//			throw LimitExceededException.newLimitExceeded(limit, sequences);
+//		}
+//		compbio.runner.Util.writeClustalInput(sequences, confExec, '-');
+//		System.out.println("WSUtil-fold: Writing the clustal input file on the server: to file: "
+//				+ confExec.getInput());
+//		System.out.println("WSUtil-fold: The executable is configured with parameters: " 
+//				+ confExec.getParameters());
+////		System.out.println("WSUTil-fold: Dump the configured executable:\n" 
+////				+ confExec.toString());
+//		AsyncExecutor engine = Configurator.getAsyncEngine(confExec);
+//		String jobId = engine.submitJob(confExec);
+//		reportUsage(confExec, logger);
+//		return jobId;
+//	}
 
 	static <T> void reportUsage(ConfiguredExecutable<T> confExec, Logger logger) {
 		if (GAUtils.IS_GA_ENABLED) {
@@ -153,8 +154,23 @@ public final class WSUtil {
 			throw LimitExceededException.newLimitExceeded(limit, sequences);
 		}
 		log.debug("Method: " + method + " with task: " + confExec.getTaskId());
-		// Change this line for RNAalifold testing
-		// compbio.runner.Util.writeInput(sequences, confExec);
+		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
+	
+	public static <T> String fold(List<FastaSequence> sequences,
+			ConfiguredExecutable<T> confExec, Logger log, String method,
+			Limit<T> limit) throws JobSubmissionException {
+		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);
@@ -193,13 +209,21 @@ public final class WSUtil {
 		}
 	}
 
-	public static <T> ScoreManager getAnnotation(String jobId, Logger log)
+	// test
+	// set return type back to ScoreManager
+	public static <T> RNAStructScoreManager getAnnotation(String jobId, Logger log)
 			throws ResultNotAvailableException {
 		WSUtil.validateJobId(jobId);
 		AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);
 		ConfiguredExecutable<T> aacon = (ConfiguredExecutable<T>) asyncEngine
 				.getResults(jobId);
-		ScoreManager mas = aacon.getResults();
+		
+		
+		// test RNAalifold
+//		ScoreManager mas = aacon.getResults();
+		
+		RNAStructScoreManager mas = aacon.getResults();
+		
 		log.trace(jobId + " getConservation : " + mas);
 		return mas;
 	}