X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=webservices%2Fcompbio%2Fws%2Fserver%2FWSUtil.java;h=07d005d3452c581a2174036095615a24e0d2b5d2;hb=bd6c0919476cff487ea479588d5ad9f3bdd5af1e;hp=7646747429b528cc177964a5800d02293e221845;hpb=42d82f347c559914cc57499c43daa49aed0573b8;p=jabaws.git

diff --git a/webservices/compbio/ws/server/WSUtil.java b/webservices/compbio/ws/server/WSUtil.java
index 7646747..07d005d 100644
--- a/webservices/compbio/ws/server/WSUtil.java
+++ b/webservices/compbio/ws/server/WSUtil.java
@@ -25,7 +25,6 @@ import java.util.Set;
 
 import org.apache.log4j.Logger;
 
-import compbio.data.sequence.Alignment;
 import compbio.data.sequence.FastaSequence;
 import compbio.data.sequence.ScoreManager;
 import compbio.engine.AsyncExecutor;
@@ -113,29 +112,6 @@ public final class WSUtil {
 		return jobId;
 	}
 	
-	// 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;
-	}
 
 	static <T> void reportUsage(ConfiguredExecutable<T> confExec, Logger logger) {
 		if (GAUtils.IS_GA_ENABLED) {
@@ -153,8 +129,25 @@ 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
+	// 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
+	
+	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);
@@ -185,10 +178,28 @@ 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());
 			}
 		}
 	}
@@ -197,12 +208,13 @@ 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