X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=webservices%2Fcompbio%2Fws%2Fserver%2FSequenceAnnotationService.java;h=afe0bf2fe38a908fb9440e661dcdad8f378fadd2;hb=68fe46f278b4ec408d6c68677bd56199aac749b3;hp=973951eb4d0c752b1806853dbd1ab3b5d806f7f6;hpb=61af8ce2cea02220228f58b30b4319f500b2f040;p=jabaws.git

diff --git a/webservices/compbio/ws/server/SequenceAnnotationService.java b/webservices/compbio/ws/server/SequenceAnnotationService.java
index 973951e..afe0bf2 100644
--- a/webservices/compbio/ws/server/SequenceAnnotationService.java
+++ b/webservices/compbio/ws/server/SequenceAnnotationService.java
@@ -1,3 +1,20 @@
+/* Copyright (c) 2011 Peter Troshin
+ *  
+ *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0     
+ * 
+ *  This library is free software; you can redistribute it and/or modify it under the terms of the
+ *  Apache License version 2 as published by the Apache Software Foundation
+ * 
+ *  This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
+ *  even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache 
+ *  License for more details.
+ * 
+ *  A copy of the license is in apache_license.txt. It is also available here:
+ * @see: http://www.apache.org/licenses/LICENSE-2.0.txt
+ * 
+ * Any republication or derived work distributed in source code form
+ * must include this copyright and license notice.
+ */
 package compbio.ws.server;
 
 import java.util.List;
@@ -43,20 +60,20 @@ public abstract class SequenceAnnotationService<T> extends GenericMetadataServic
 		return WSUtil.getAnnotation(jobId, log);
 	}
 
+	@SuppressWarnings("unchecked")
 	public String analize(List<FastaSequence> sequences)
-			throws UnsupportedRuntimeException, LimitExceededException,
-			JobSubmissionException {
+			throws UnsupportedRuntimeException, LimitExceededException, JobSubmissionException {
 		WSUtil.validateFastaInput(sequences);
 		ConfiguredExecutable<T> confIUPred = init(sequences);
-		return WSUtil.analize(sequences, confIUPred, log, "analize",
-				getLimit(""));
+		return WSUtil.analize(sequences, confIUPred, log, "analize", getLimit(""));
 	}
 
+	@SuppressWarnings("unchecked")
 	public String customAnalize(List<FastaSequence> sequences,
 			List<Option<T>> options) throws UnsupportedRuntimeException,
 			LimitExceededException, JobSubmissionException,
 			WrongParameterException {
-		WSUtil.validateAAConInput(sequences);
+		WSUtil.validateFastaInput(sequences);
 		ConfiguredExecutable<T> confAACon = init(sequences);
 		// Could not do that! Space separated values
 		// will all be treated as keys! thus duplicates removed
@@ -64,22 +81,20 @@ public abstract class SequenceAnnotationService<T> extends GenericMetadataServic
 		List<String> params = WSUtil.getCommands(options,
 				AACon.KEY_VALUE_SEPARATOR);
 		confAACon.addParameters(params);
-		return WSUtil.analize(sequences, confAACon, log, "customAnalize",
-				getLimit(""));
+		return WSUtil.analize(sequences, confAACon, log, "customAnalize", getLimit(""));
 	}
 
 	public String presetAnalize(List<FastaSequence> sequences, Preset<T> preset)
-			throws UnsupportedRuntimeException, LimitExceededException,
-			JobSubmissionException, WrongParameterException {
+			throws UnsupportedRuntimeException, LimitExceededException, JobSubmissionException, WrongParameterException {
 		WSUtil.validateAAConInput(sequences);
 		if (preset == null) {
 			throw new WrongParameterException("Preset must be provided!");
 		}
+		@SuppressWarnings("unchecked")
 		ConfiguredExecutable<T> confAAcon = init(sequences);
 		confAAcon.addParameters(preset.getOptions());
+		@SuppressWarnings("unchecked")
 		Limit<T> limit = getLimit(preset.getName());
-		return WSUtil
-				.analize(sequences, confAAcon, log, "presetAnalize", limit);
+		return WSUtil.analize(sequences, confAAcon, log, "presetAnalize", limit);
 	}
-
 }