X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=datadb%2Fcompbio%2Fcassandra%2FJpredParserHTTP.java;h=d03ac7999384cc0fec99f299625d266602a7fc1c;hb=3887e427255a9ed5e9e43f4a52a377935331e5d3;hp=052ff6ad457bddb194925332aa57ec367ec0e9dd;hpb=7f8e9a42b27028e6efecee7819f21c7b38f42f34;p=proteocache.git

diff --git a/datadb/compbio/cassandra/JpredParserHTTP.java b/datadb/compbio/cassandra/JpredParserHTTP.java
index 052ff6a..d03ac79 100644
--- a/datadb/compbio/cassandra/JpredParserHTTP.java
+++ b/datadb/compbio/cassandra/JpredParserHTTP.java
@@ -1,6 +1,7 @@
 package compbio.cassandra;
 
 import java.io.BufferedReader;
+import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.io.InputStreamReader;
 import java.net.HttpURLConnection;
@@ -17,7 +18,7 @@ import java.util.List;
 import compbio.cassandra.JpredParser;
 
 public class JpredParserHTTP implements JpredParser {
-	private CassandraCreate cc = new CassandraCreate();
+	private CassandraNativeConnector cc = new CassandraNativeConnector();
 	private String dirprefix;
 
 	JpredParserHTTP() {
@@ -32,7 +33,7 @@ public class JpredParserHTTP implements JpredParser {
 		dirprefix = newsourceprefix;
 	}
 
-	public void Parsing(String source, int nDays) {
+	public void Parsing(String source, int nDays) throws IOException {
 		Calendar cal = Calendar.getInstance();
 		cal.add(Calendar.DATE, -nDays);
 		for (int i = 0; i < nDays; ++i) {
@@ -41,9 +42,7 @@ public class JpredParserHTTP implements JpredParser {
 			int year = cal.get(Calendar.YEAR);
 			int day = cal.get(Calendar.DATE);
 			String date = year + "/" + month + "/" + day;
-			if (0 < ParsingForDate(source, date)) {
-				cc.flushData();
-			}
+			ParsingForDate(source, date);
 		}
 	}
 
@@ -86,8 +85,9 @@ public class JpredParserHTTP implements JpredParser {
 									final FastaSequence fs = fr.next();
 									if (fs.getId().equals("QUERY") || fs.getId().equals(id))
 										newprotein = fs.getSequence().replaceAll("\n", "");
-									else
+									else if (fs.getId().equals("jnetpred") || fs.getId().equals("JNETPRED")) {
 										seqs.add(fs);
+									}
 								}
 								if (newprotein.equals("")) {
 									countUnclearFASTAid++;
@@ -105,10 +105,10 @@ public class JpredParserHTTP implements JpredParser {
 									++countinsertions;
 									++njobs;
 									// flush every 50 insertions
-									if (0 == countinsertions % 50) {
-										cc.flushData();
-										njobs -= 50;
-									}
+									//if (0 == countinsertions % 50) {
+									//	cc.flushData();
+									//	njobs -= 50;
+									//}
 								}
 							} catch (IOException e) {
 								e.printStackTrace();