X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=datadb%2Fcompbio%2Fcassandra%2FJpredParserLocalFile.java;h=281a20bdb604ef99e07fc6974bbed47b821235f5;hb=26b5b869bd204707a825e457a14f61e1d8ab0750;hp=27d4252c19d5e9594de6742f1dda011d7901e7d7;hpb=3887e427255a9ed5e9e43f4a52a377935331e5d3;p=proteocache.git

diff --git a/datadb/compbio/cassandra/JpredParserLocalFile.java b/datadb/compbio/cassandra/JpredParserLocalFile.java
index 27d4252..281a20b 100644
--- a/datadb/compbio/cassandra/JpredParserLocalFile.java
+++ b/datadb/compbio/cassandra/JpredParserLocalFile.java
@@ -77,53 +77,43 @@ public class JpredParserLocalFile implements JpredParser {
 				String ip = table[2];
 				String id = table[table.length - 1];
 				totalcount++;
-				//if (!cc.CheckID(id)) {
-					if (true) {
-					String confilename = dirprefix + "/" + id + "/" + id + ".concise";
-					File confile = new File(confilename);
-					if (confile.exists()) {
-						try {
-							final FastaReader fr = new FastaReader(confilename);
-							final List<FastaSequence> seqs = new ArrayList<FastaSequence>();
-							String newprotein = "";
-							while (fr.hasNext()) {
-								final FastaSequence fs = fr.next();
-								if (fs.getId().equals("QUERY") || fs.getId().equals(id))
-									newprotein = fs.getSequence().replaceAll("\n", "");
-								else if (fs.getId().equals("jnetpred") || fs.getId().equals("JNETPRED")) {
-									seqs.add(fs);
-								}
+				String confilename = dirprefix + "/" + id + "/" + id + ".concise";
+				File confile = new File(confilename);
+				if (confile.exists()) {
+					try {
+						final FastaReader fr = new FastaReader(confilename);
+						final List<FastaSequence> seqs = new ArrayList<FastaSequence>();
+						String newprotein = "";
+						while (fr.hasNext()) {
+							final FastaSequence fs = fr.next();
+							if (fs.getId().equals("QUERY") || fs.getId().equals(id))
+								newprotein = fs.getSequence().replaceAll("\n", "");
+							else if (fs.getId().equals("jnetpred") || fs.getId().equals("JNETPRED")) {
+								seqs.add(fs);
 							}
-							if (newprotein.equals("")) {
-								countUnclearFASTAid++;
-							} else {
-								SimpleDateFormat formatter = new SimpleDateFormat("yyyy/MM/dd");
-								String dateInString1 = starttime.substring(0, starttime.indexOf(":"));
-								long dateWork1 = 0;
-								try {
-									Date dat = formatter.parse(dateInString1);
-									dateWork1 = dat.getTime();
-								} catch (ParseException e) {
-									e.printStackTrace();
-								}
-								cc.InsertData(dateWork1, starttime, finishtime, ip, id, "OK", "OK", newprotein, seqs);
-								++countinsertions;
-								++njobs;
-								// flush every 50 insertions
-								//if (0 == countinsertions % 50) {
-								//	cc.flushData();
-								//	njobs -= 50;
-								//}
+						}
+						if (newprotein.equals("")) {
+							countUnclearFASTAid++;
+						} 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();
 							}
-							fr.close();
-						} catch (IOException e) {
-							e.printStackTrace();
+							cc.InsertData(insertdate, starttime, finishtime, ip, id, "OK", "OK", newprotein, seqs);
+							++countinsertions;
+							++njobs;
 						}
-					} else {
-						countNoData++;
+						fr.close();
+					} catch (IOException e) {
+						e.printStackTrace();
 					}
 				} else {
-					++countinserted;
+					countNoData++;
 				}
 			} else {
 				if (in.matches(date + "(.*)Sequence0/(.*)")) {