Add new still not-working code for native binary protocol version

[proteocache.git] / datadb / compbio / cassandra / JpredParserHTTP.java

diff --git a/datadb/compbio/cassandra/JpredParserHTTP.java b/datadb/compbio/cassandra/JpredParserHTTP.java
index 052ff6a..d03ac79 100644 (file)
--- 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();