Clean up the code

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

diff --git a/datadb/compbio/cassandra/JpredParserLocalFile.java b/datadb/compbio/cassandra/JpredParserLocalFile.java
index 281a20b..c89fe59 100644 (file)
--- 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;
        }
 
 }