From: Sasha Sherstnev <a.sherstnev@dundee.ac.uk>
Date: Mon, 28 Oct 2013 20:22:05 +0000 (+0000)
Subject: Remove surplus code and add format of the source file
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=2260ca3b3c0382ef6bfeea7341a692508058a2a6;p=proteocache.git

Remove surplus code and add format of the source file
---

diff --git a/datadb/compbio/cassandra/JpredParserHTTP.java b/datadb/compbio/cassandra/JpredParserHTTP.java
index 3616818..e308a25 100644
--- a/datadb/compbio/cassandra/JpredParserHTTP.java
+++ b/datadb/compbio/cassandra/JpredParserHTTP.java
@@ -19,17 +19,17 @@ import compbio.cassandra.JpredParser;
 public class JpredParserHTTP implements JpredParser {
 	private CassandraCreate cc = new CassandraCreate();
 	private String dirprefix;
-	
+
 	JpredParserHTTP() {
-		this.dirprefix = "http://www.compbio.dundee.ac.uk/www-jpred/results";
+		dirprefix = "http://www.compbio.dundee.ac.uk/www-jpred/results";
 	}
-	
+
 	JpredParserHTTP(String sourceurl) {
-		this.dirprefix = sourceurl;
+		dirprefix = sourceurl;
 	}
 
-	public void setSource (String newsourceprefix) {
-		this.dirprefix = newsourceprefix;
+	public void setSource(String newsourceprefix) {
+		dirprefix = newsourceprefix;
 	}
 
 	public void Parsing(String source, int nDays) {
@@ -64,10 +64,14 @@ public class JpredParserHTTP implements JpredParser {
 			while ((line = alljobs.readLine()) != null) {
 				if (line.matches(date + "(.*)jp_[^\\s]+")) {
 					String[] table = line.split("\\s+");
+					// Format of a record:
+					// starttime endtime ip email jobid (directory)
+					// 013/10/25:21:55:7 2013/10/25:21:59:13 201.239.98.172 unknown_email jp_J9HBCBT
 					String id = table[table.length - 1];
 					totalcount++;
 					if (!cc.CheckID(id)) {
-						URL urltable = new URL(dirprefix + "/" + id + "/" + id + ".concise.fasta");
+						String datalink = dirprefix + "/" + id + "/" + id + ".concise.fasta";
+						URL urltable = new URL(datalink);
 						HttpURLConnection httpConnection = (HttpURLConnection) urltable.openConnection();
 						int responsecode = httpConnection.getResponseCode();
 						if (199 < responsecode && responsecode < 300) {