X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=datadb%2Fcompbio%2Fcassandra%2FJpredParserLocalFile.java;h=c89fe5999c6e1e8869d4e465fea0e7837ca4549e;hb=75431c815ea42cf3ffa18f485721146636575265;hp=281a20bdb604ef99e07fc6974bbed47b821235f5;hpb=7fafa396b8b56bb5cc7249dc7c12fd37edf5724b;p=proteocache.git

diff --git a/datadb/compbio/cassandra/JpredParserLocalFile.java b/datadb/compbio/cassandra/JpredParserLocalFile.java
index 281a20b..c89fe59 100644
--- a/datadb/compbio/cassandra/JpredParserLocalFile.java
+++ b/datadb/compbio/cassandra/JpredParserLocalFile.java
@@ -2,11 +2,8 @@ package compbio.cassandra;
 
 import java.io.BufferedReader;
 import java.io.File;
-import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.io.InputStreamReader;
-import java.net.HttpURLConnection;
-import java.net.MalformedURLException;
 import java.io.FileInputStream;
 import java.text.ParseException;
 import java.text.SimpleDateFormat;
@@ -15,19 +12,21 @@ import java.util.Calendar;
 import java.util.Date;
 import java.util.List;
 
+import compbio.data.sequence.FastaReader;
+import compbio.data.sequence.FastaSequence;
+
 public class JpredParserLocalFile implements JpredParser {
-	private CassandraNativeConnector cc = new CassandraNativeConnector();
 	private String dirprefix;
 
 	public void setSource(String newsourceprefix) {
 		this.dirprefix = newsourceprefix;
 	}
 
-	JpredParserLocalFile() {
+	public JpredParserLocalFile() {
 		this.dirprefix = "/home/asherstnev/Projects/Java.projects/proteocache/data_stress_test/data.dat";
 	}
 
-	JpredParserLocalFile(String sourceurl) {
+	public JpredParserLocalFile(String sourceurl) {
 		this.dirprefix = sourceurl;
 	}
 
@@ -58,7 +57,7 @@ public class JpredParserLocalFile implements JpredParser {
 		System.out.println("Execution Time = " + execTime + " ms");
 	}
 
-	private int ParsingForDate(List<String> input, String date) {
+	private void ParsingForDate(List<String> input, String date) {
 		int totalcount = 0;
 		int countNoData = 0;
 		int countUnclearFASTAid = 0;
@@ -66,15 +65,12 @@ public class JpredParserLocalFile implements JpredParser {
 		int countinserted = 0;
 		int counAlignments = 0;
 		int countStrange = 0;
-		int njobs = 0;
 
 		System.out.println("Inserting jobs for " + date);
 		for (String in : input) {
-			if (in.matches(date + "(.*)jp_[^\\s]+")) {
+			if (in.matches(date + ":(.*)jp_[^\\s]+")) {
 				String[] table = in.split("\\s+");
 				String starttime = table[0];
-				String finishtime = table[1];
-				String ip = table[2];
 				String id = table[table.length - 1];
 				totalcount++;
 				String confilename = dirprefix + "/" + id + "/" + id + ".concise";
@@ -97,16 +93,14 @@ public class JpredParserLocalFile implements JpredParser {
 						} else {
 							SimpleDateFormat formatter = new SimpleDateFormat("yyyy/MM/dd");
 							String dateInString1 = starttime.substring(0, starttime.indexOf(":"));
-							long insertdate = 0;
 							try {
 								Date dat = formatter.parse(dateInString1);
-								insertdate = dat.getTime();
 							} catch (ParseException e) {
 								e.printStackTrace();
 							}
-							cc.InsertData(insertdate, starttime, finishtime, ip, id, "OK", "OK", newprotein, seqs);
-							++countinsertions;
-							++njobs;
+							// countinsertions += cw.FormQueryTables(insertdate,
+							// starttime, finishtime, ip, id, "OK", "OK",
+							// newprotein, seqs);
 						}
 						fr.close();
 					} catch (IOException e) {
@@ -132,7 +126,6 @@ public class JpredParserLocalFile implements JpredParser {
 			System.out.println("   " + countUnclearFASTAid + " jobs with unclear FASTA protein id in *.concise.fasta");
 			System.out.println("   " + countinsertions + " new job insertions\n");
 		}
-		return njobs;
 	}
 
 }