From d533fe6c1adf9f81009386ce42a9beb6999f7c3c Mon Sep 17 00:00:00 2001
From: Sasha Sherstnev <a.sherstnev@dundee.ac.uk>
Date: Fri, 31 Jan 2014 16:51:47 +0000
Subject: [PATCH] Add documentation to the classes

---
 server/compbio/ws/jpred/Jpred.java   |   41 ++++++++++++++++++++++++++++++++++
 server/compbio/ws/jpred/JpredWS.java |   12 +++++++++-
 2 files changed, 52 insertions(+), 1 deletion(-)

diff --git a/server/compbio/ws/jpred/Jpred.java b/server/compbio/ws/jpred/Jpred.java
index 4b4a965..72b1a9e 100644
--- a/server/compbio/ws/jpred/Jpred.java
+++ b/server/compbio/ws/jpred/Jpred.java
@@ -4,17 +4,58 @@ import javax.jws.WebMethod;
 import javax.jws.WebParam;
 import javax.jws.WebService;
 
+/**
+ * Jpred interface of the corresponding web serice in ProteoCache
+ * 
+ * @author Alexander Sherstnev
+ * @author Natasha Sherstneva
+ * 
+ * @version 1.0
+ * @since Jan 2014
+ */
 @WebService(targetNamespace = "http://server.proteocache.ws")
 public interface Jpred {
 
+	/**
+	 * Returns a number of jobs xecuted for a protein with a program of a
+	 * version
+	 * 
+	 * @param sequence
+	 *            the protein sequence
+	 * @param program
+	 *            the program title
+	 * @param version
+	 *            the program version
+	 * @return a number of jobs executed for the protein
+	 */
 	@WebMethod
 	public String findSequence(@WebParam(name = "sequence") String sequence, @WebParam(name = "program") String program,
 			@WebParam(name = "version") String version);
 
+	/**
+	 * Returns a job ID executed for a protein with a program of a version if
+	 * the job archive file is available, otherwise returns empty string
+	 * 
+	 * @param sequence
+	 *            the protein sequence
+	 * @param program
+	 *            the program title
+	 * @param version
+	 *            the program version
+	 * @return job ID
+	 */
 	@WebMethod
 	public String findJobForSequence(@WebParam(name = "sequence") String sequence, @WebParam(name = "program") String program,
 			@WebParam(name = "version") String version);
 
+	/**
+	 * Returns a relative web link to the job archive file for a ProteoCache
+	 * job, if the file is not available null is returned
+	 * 
+	 * @param jobid
+	 *            the job ID
+	 * @return the job archive file web link or null
+	 */
 	@WebMethod
 	public String getArchive(@WebParam(name = "job") String jobid);
 }
diff --git a/server/compbio/ws/jpred/JpredWS.java b/server/compbio/ws/jpred/JpredWS.java
index 9978cc4..5249280 100644
--- a/server/compbio/ws/jpred/JpredWS.java
+++ b/server/compbio/ws/jpred/JpredWS.java
@@ -13,6 +13,15 @@ import compbio.cassandra.CassandraNativeConnector;
 import compbio.cassandra.readers.SequenceReader;
 import compbio.engine.archive.ArchivedJob;
 
+/**
+ * Implementation of the Jpred web service in ProteoCache
+ * 
+ * @author Alexander Sherstnev
+ * @author Natasha Sherstneva
+ * 
+ * @version 1.0
+ * @since Jan 2014
+ */
 @WebService(endpointInterface = "compbio.ws.jpred.Jpred", targetNamespace = "http://server.proteocache.ws", serviceName = "ProteoCacheWS", portName = "ProteoCacheWSPort")
 public class JpredWS implements Jpred {
 	private static Logger log = Logger.getLogger(CassandraNativeConnector.class);
@@ -71,7 +80,7 @@ public class JpredWS implements Jpred {
 
 	@Override
 	public String getArchive(String jobid) {
-		String link = "undefined";
+		String link = null;
 		ArchivedJob aj = new ArchivedJob(jobid);
 		try {
 			link = aj.prepareJobArchiveToWeb();
@@ -79,6 +88,7 @@ public class JpredWS implements Jpred {
 			log.error("JpredWS.findSequence: IO exception with job archive file");
 			log.error(e.getLocalizedMessage(), e.getCause());
 		}
+		// if the archive file is not available null is returned
 		return link;
 	}
 
-- 
1.7.10.2