From 75431c815ea42cf3ffa18f485721146636575265 Mon Sep 17 00:00:00 2001
From: Sasha Sherstnev <a.sherstnev@dundee.ac.uk>
Date: Mon, 27 Jan 2014 14:53:16 +0000
Subject: [PATCH] Clean up the code

---
 datadb/compbio/beans/DateBean.java                 |    1 -
 datadb/compbio/cassandra/DataBase.java             |    2 --
 datadb/compbio/cassandra/JpredParserLocalFile.java |    8 --------
 engine/compbio/engine/ExecutionInterval.java       |    1 -
 engine/compbio/engine/JpredJob.java                |    2 --
 server/compbio/statistic/CassandraRequester.java   |   13 ++++++-------
 6 files changed, 6 insertions(+), 21 deletions(-)

diff --git a/datadb/compbio/beans/DateBean.java b/datadb/compbio/beans/DateBean.java
index 7c593d3..b00e1d6 100644
--- a/datadb/compbio/beans/DateBean.java
+++ b/datadb/compbio/beans/DateBean.java
@@ -1,7 +1,6 @@
 package compbio.beans;
 
 import java.util.HashMap;
-import java.util.LinkedHashMap;
 import java.util.Map;
 
 public class DateBean {
diff --git a/datadb/compbio/cassandra/DataBase.java b/datadb/compbio/cassandra/DataBase.java
index e741b39..6ced180 100644
--- a/datadb/compbio/cassandra/DataBase.java
+++ b/datadb/compbio/cassandra/DataBase.java
@@ -1,8 +1,6 @@
 package compbio.cassandra;
 
 import java.util.List;
-import java.util.ArrayList;
-import java.util.Collections;
 
 import compbio.beans.JobBean;
 import compbio.beans.ProteinBean;
diff --git a/datadb/compbio/cassandra/JpredParserLocalFile.java b/datadb/compbio/cassandra/JpredParserLocalFile.java
index e2e5dc9..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;
@@ -19,7 +16,6 @@ import compbio.data.sequence.FastaReader;
 import compbio.data.sequence.FastaSequence;
 
 public class JpredParserLocalFile implements JpredParser {
-	private CassandraWriter cw = new CassandraWriter();
 	private String dirprefix;
 
 	public void setSource(String newsourceprefix) {
@@ -75,8 +71,6 @@ public class JpredParserLocalFile implements JpredParser {
 			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";
@@ -99,10 +93,8 @@ 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();
 							}
diff --git a/engine/compbio/engine/ExecutionInterval.java b/engine/compbio/engine/ExecutionInterval.java
index 9b0bcee..79b7cb0 100644
--- a/engine/compbio/engine/ExecutionInterval.java
+++ b/engine/compbio/engine/ExecutionInterval.java
@@ -1,6 +1,5 @@
 package compbio.engine;
 
-import compbio.cassandra.Pair;
 
 
 /**
diff --git a/engine/compbio/engine/JpredJob.java b/engine/compbio/engine/JpredJob.java
index 522ad9f..99981e4 100644
--- a/engine/compbio/engine/JpredJob.java
+++ b/engine/compbio/engine/JpredJob.java
@@ -17,7 +17,6 @@ public class JpredJob extends Job {
 
 	public JpredJob(String jobid, String date1, String date2) {
 		super(jobid, date1, date2);
-		this.protein = protein;
 		predictions = new ArrayList<FastaSequence>();
 		alignment = new ArrayList<FastaSequence>();
 		log = "";
@@ -25,7 +24,6 @@ public class JpredJob extends Job {
 
 	public JpredJob(String jobid, String date1, String date2, List<FastaSequence> alignment, List<FastaSequence> predictions) {
 		super(jobid, date1, date2);
-		this.protein = protein;
 		this.alignment = alignment;
 		this.predictions = predictions;
 	}
diff --git a/server/compbio/statistic/CassandraRequester.java b/server/compbio/statistic/CassandraRequester.java
index ca59844..1791c0f 100755
--- a/server/compbio/statistic/CassandraRequester.java
+++ b/server/compbio/statistic/CassandraRequester.java
@@ -19,8 +19,8 @@ import compbio.beans.UserBean;
 import compbio.cassandra.CassandraNativeConnector;
 import compbio.cassandra.CassandraReaderOld;
 import compbio.cassandra.DataBase;
-import compbio.cassandra.Pair;
 import compbio.engine.JobStatus;
+import compbio.engine.Pair;
 
 public class CassandraRequester {
 	private CassandraReaderOld db = new CassandraReaderOld();
@@ -112,17 +112,16 @@ public class CassandraRequester {
 			query.add(db);
 		}
 
-		/* ???? Very strange code...
-		DataBase db = new DataBase();
-		db.setTimeTotalExec(totalTime);
-		query.add(db);
-		*/
+		/*
+		 * ???? Very strange code... DataBase db = new DataBase();
+		 * db.setTimeTotalExec(totalTime); query.add(db);
+		 */
 		return query;
 	}
 
 	/*
 	 * query: total number of jobs for the period from date1 till date2
-	*/ 
+	 */
 	public TotalJobsStatisticBean countJobs(String date1, String date2) {
 		/*
 		 * if (null == date1) { date1 = "1970/1/1"; } if (null == date2) { date1
-- 
1.7.10.2