JWS-113 Commented Jpred entries in the datamodel, runner and webservices java source...

[jabaws.git] / webservices / compbio / ws / server / SequenceAnnotationService.java

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