From: Sasha Sherstnev <a.sherstnev@dundee.ac.uk>
Date: Fri, 15 Nov 2013 11:31:27 +0000 (+0000)
Subject: PROT-1 Prepare project for Maven build system
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=008be2cc63154bacbe1cbf5fa03ffbe49fdc09da;p=proteocache.git

PROT-1 Prepare project for Maven build system
---

diff --git a/README.txt b/README.txt
new file mode 100644
index 0000000..0bc6883
--- /dev/null
+++ b/README.txt
@@ -0,0 +1 @@
+ProteoCache is a project for caching data from Jpred
diff --git a/pom.xml b/pom.xml
new file mode 100644
index 0000000..ae3f19b
--- /dev/null
+++ b/pom.xml
@@ -0,0 +1,22 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+  xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+	<groupId>compbio</groupId>
+	<artifactId>proteocache</artifactId>
+	<packaging>war</packaging>
+	<version>0.1.0-SNAPSHOT</version>
+	<name>proteocache</name>
+	<url>http://maven.apache.org</url>
+
+
+
+
+  <dependencies>
+    <dependency>
+      <groupId>junit</groupId>
+      <artifactId>junit</artifactId>
+      <version>3.8.1</version>
+      <scope>test</scope>
+    </dependency>
+  </dependencies>
+</project>
diff --git a/src/main/java/compbio/cassandra/CassandraNativeConnector.java b/src/main/java/compbio/cassandra/CassandraNativeConnector.java
new file mode 100644
index 0000000..9d214ec
--- /dev/null
+++ b/src/main/java/compbio/cassandra/CassandraNativeConnector.java
@@ -0,0 +1,101 @@
+package compbio.cassandra;
+
+import java.util.Calendar;
+
+import org.apache.log4j.Logger;
+
+import com.datastax.driver.core.Cluster;
+import com.datastax.driver.core.Host;
+import com.datastax.driver.core.Metadata;
+import com.datastax.driver.core.ResultSet;
+import com.datastax.driver.core.Row;
+
+import com.datastax.driver.core.Session;
+import compbio.engine.ProteoCachePropertyHelperManager;
+import compbio.util.PropertyHelper;
+
+public class CassandraNativeConnector {
+	private static Cluster cluster;
+	private static Session session;
+	private static final PropertyHelper ph = ProteoCachePropertyHelperManager.getPropertyHelper();
+	private static Logger log = Logger.getLogger(CassandraNativeConnector.class);
+
+	public static String CASSANDRA_HOSTNAME = "localhost";
+
+	public static Session getSession () {
+		return session;
+	}
+
+	/*
+	 * connect to the cluster and look whether all tables exist
+	 */
+	public void Connect() {
+
+		String cassandrahostname = ph.getProperty("cassandra.host");
+		if (null != cassandrahostname) {
+			CASSANDRA_HOSTNAME = cassandrahostname;
+		}
+
+		cluster = Cluster.builder().addContactPoint(CASSANDRA_HOSTNAME).build();
+
+		Metadata metadata = cluster.getMetadata();
+		System.out.printf("Connected to cluster: %s\n", metadata.getClusterName());
+		for (Host host : metadata.getAllHosts()) {
+			System.out.printf("Datatacenter: %s; Host: %s; Rack: %s\n", host.getDatacenter(), host.getAddress(), host.getRack());
+		}
+		session = cluster.connect();
+		CreateMainTables();
+		System.out.println("Cassandra connected");
+	}
+
+	private void CreateMainTables() {
+		session.execute("CREATE KEYSPACE IF NOT EXISTS ProteinKeyspace WITH replication = {'class':'SimpleStrategy', 'replication_factor':3};");
+		session.execute("USE ProteinKeyspace");
+
+		session.execute("CREATE TABLE IF NOT EXISTS MainParameters "
+				+ "(Name ascii, Value ascii, PRIMARY KEY(Name));");
+		
+		session.execute("CREATE TABLE IF NOT EXISTS ProteinRow "
+				+ "(Protein ascii, JobID ascii, Predictions map<ascii,ascii>, PRIMARY KEY(JobID));");
+
+		session.execute("CREATE TABLE IF NOT EXISTS ProteinLog "
+				+ "(JobID ascii, DataBegin ascii, DataEnd ascii, ip ascii, FinalStatus ascii, "
+				+ "ExecutionStatus ascii, Protein ascii, PRIMARY KEY(JobID));");
+
+		session.execute("CREATE TABLE IF NOT EXISTS ProteinData "
+				+ "(jobtime bigint, JobID ascii, Protein ascii, PRIMARY KEY(JobID));");
+
+		session.execute("CREATE TABLE IF NOT EXISTS JpredArchive "
+				+ "(JobID ascii, Protein varchar, IP ascii, StartTime bigint, ExecTime int, alignment map<ascii,ascii>, "
+				+ "predictions map<ascii,ascii>, ArchiveLink varchar, LOG varchar, PRIMARY KEY(JobID));");
+		
+		session.execute("CREATE TABLE IF NOT EXISTS JobDateInfo "
+				+ "(jobday bigint, Total bigint, Program varchar, Version varchar, PRIMARY KEY(jobday));");
+
+		session.execute("CREATE INDEX IF NOT EXISTS ProteinSeq ON ProteinRow (protein);");
+		session.execute("CREATE INDEX IF NOT EXISTS JobDateStamp ON ProteinData (jobtime);");
+	}
+
+	public void Closing() {
+		session.shutdown();
+		cluster.shutdown();
+		System.out.println("Cassandra has been shut down");
+	}
+
+	/*
+	 * getting earlest date of jobs from the db
+	 */
+	public static long getEarliestDateInDB() {
+		String com = "SELECT * FROM MainParameters WHERE Name = 'EarliestJobDate';";
+		System.out.println("Command: " + com);
+		ResultSet results = session.execute(com);
+
+		if (!results.isExhausted()) {
+			Row r = results.one();
+			return Long.parseLong(r.getString("Value"));
+		}
+		Calendar cal = Calendar.getInstance();
+		return cal.getTimeInMillis();
+	}
+	
+}
diff --git a/src/main/java/compbio/cassandra/CassandraNewTableWriter.java b/src/main/java/compbio/cassandra/CassandraNewTableWriter.java
new file mode 100644
index 0000000..0d68b1a
--- /dev/null
+++ b/src/main/java/compbio/cassandra/CassandraNewTableWriter.java
@@ -0,0 +1,95 @@
+package compbio.cassandra;
+
+import java.util.Calendar;
+import java.util.Date;
+
+import org.apache.log4j.Logger;
+
+import com.datastax.driver.core.Row;
+import com.datastax.driver.core.Session;
+import com.datastax.driver.core.ResultSet;
+import com.datastax.driver.core.PreparedStatement;
+import com.datastax.driver.core.BoundStatement;
+import com.datastax.driver.core.exceptions.QueryExecutionException;
+
+import compbio.engine.ProteoCachePropertyHelperManager;
+import compbio.cassandra.CassandraNativeConnector;
+
+public class CassandraNewTableWriter {
+	private Session session;
+	private static Logger log = Logger.getLogger(CassandraNativeConnector.class);
+
+	public CassandraNewTableWriter() {
+		Session inis = CassandraNativeConnector.getSession();
+		setSession(inis);
+	}
+
+	public void setSession(Session s) {
+		assert s != null;
+		session = s;
+	}
+
+	public boolean JobisNotInsterted(String jobid) {
+		ResultSet results1 = session.execute("SELECT * FROM ProteinLog WHERE JobID = '" + jobid + "';");
+		if (results1.isExhausted()) {
+			return true;
+		}
+		return false;
+	}
+
+	public boolean JobisNotArchived(String jobid) {
+		ResultSet results1 = session.execute("SELECT * FROM JpredArchive WHERE JobID = '" + jobid + "';");
+		if (results1.isExhausted()) {
+			return true;
+		}
+		return false;
+	}
+
+	/*
+	 * fill new table
+	 */
+	public void FillNewTable() {
+		final long StartTime = System.currentTimeMillis();
+		long erldate = CassandraNativeConnector.getEarliestDateInDB();
+		Calendar runnicCal = Calendar.getInstance();
+		runnicCal.setTime(new Date(erldate));
+		Calendar endcal = Calendar.getInstance();
+		long endTime = endcal.getTime().getTime();
+		for (Date date = runnicCal.getTime(); date.getTime() < endTime; runnicCal.add(Calendar.DATE, 1), date = runnicCal.getTime()) {
+			try {
+				ResultSet results = session.execute("SELECT * FROM ProteinData WHERE jobtime = " + date.getTime() + ";");
+				session.execute("INSERT INTO JobDateInfo " + "(jobday, Total)" + " VALUES (" + date.getTime() + "," + results.all().size()
+						+ ");");
+			} catch (QueryExecutionException e) {
+				e.printStackTrace();
+			}
+		}
+		System.out.println("Table JobDateInfo filled: total time is " + (System.currentTimeMillis() - StartTime) + " msec");
+	}
+
+	/*
+	 * fill a table with the database global parameters
+	 */
+	public void FillMainDBParameters() {
+		Date bubu = new Date(CassandraNativeConnector.getEarliestDateInDB());
+		System.out.println("Old EarliestJobDate is " + bubu.toString());
+
+		String query1 = "SELECT jobtime FROM ProteinData LIMIT 2000000;";
+		System.out.println("Query db: " + query1);
+		ResultSet results = session.execute(query1);
+		Calendar endcal = Calendar.getInstance();
+		long newearliestday = endcal.getTime().getTime();
+		while (!results.isExhausted()) {
+			Row r = results.one();
+			long day = r.getLong("jobtime");
+			if (day < newearliestday) {
+				newearliestday = day;
+			}
+		}
+		String com = "INSERT INTO MainParameters " + "(Name, Value)" + " VALUES ('EarliestJobDate','" + String.valueOf(newearliestday)
+				+ "');";
+		session.execute(com);
+		Date gaga = new Date(newearliestday);
+		System.out.println("New EarliestJobDate is " + gaga.toString());
+	}
+}
diff --git a/src/main/java/compbio/cassandra/CassandraReader.java b/src/main/java/compbio/cassandra/CassandraReader.java
new file mode 100644
index 0000000..af697a0
--- /dev/null
+++ b/src/main/java/compbio/cassandra/CassandraReader.java
@@ -0,0 +1,178 @@
+package compbio.cassandra;
+
+import java.util.Date;
+import java.util.HashMap;
+import java.util.List;
+import java.util.ArrayList;
+import java.util.Map;
+
+import org.apache.log4j.Logger;
+
+import com.datastax.driver.core.Row;
+import com.datastax.driver.core.Session;
+import com.datastax.driver.core.ResultSet;
+
+public class CassandraReader {
+	private Session session;
+	private static Logger log = Logger.getLogger(CassandraNativeConnector.class);
+
+	public CassandraReader() {
+		Session inis = CassandraNativeConnector.getSession();
+		setSession (inis);
+	}
+
+	public void setSession(Session s) {
+		assert s != null;
+		session = s;
+	}
+
+	/*
+	 * getting data from the db
+	 */
+	public List<Pair<String, String>> ReadProteinDataTable() {
+		final long startTime = System.currentTimeMillis();
+		String com = "SELECT DataBegin,DataEnd FROM ProteinLog;";
+		System.out.println("Command: " + com);
+		ResultSet results = session.execute(com);
+		final long queryTime = System.currentTimeMillis();
+		List<Row> rows = results.all();
+		System.out.println("Query time is " + (queryTime - startTime) + " msec");
+
+		List<Pair<String, String>> res = new ArrayList<Pair<String, String>>();
+		int c = 0;
+		for (Row r : rows) {
+			Pair<String, String> pair = new Pair<String, String>(r.getString("DataBegin"), r.getString("DataEnd"));
+			res.add(pair);
+			++c;
+		}
+		final long endTime = System.currentTimeMillis();
+		System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
+		return res;
+	}
+
+	/*
+	 * getting data from the db JobDateInfo
+	 */
+	public long ReadDateTable(long queryDate) {
+		ResultSet results = session.execute("SELECT Total FROM JobDateInfo WHERE jobday = " + queryDate + ";");
+		if (results.isExhausted())
+			return 0;
+		Row therow = results.one();
+		long res = therow.getLong("Total");
+		if (!results.isExhausted()) {
+			Date date = new Date (queryDate);
+			log.warn("CassandraReader.ReadDateTable: date row for " + date.toString () + " ("+ queryDate + ") duplicated ");
+		}
+		return res;
+	}
+	/*
+	 * getting whole protein sequence from the db ProteinRow
+	 */
+	public List<StructureProteinPrediction> ReadWholeSequence(String queryProtein) {
+		final long startTime = System.currentTimeMillis();
+		String com = "SELECT JobID, Predictions FROM ProteinRow WHERE Protein = '" + queryProtein + "';";
+		System.out.println("Command: " + com);
+		ResultSet results = session.execute(com);
+		if (results.isExhausted())
+			return null;
+		final long queryTime = System.currentTimeMillis();
+		List<Row> rows = results.all();
+		System.out.println("Query time is " + (queryTime - startTime) + " msec");
+		System.out.println(" rows analysed,  " + rows.size());
+		List<StructureProteinPrediction> res = new ArrayList<StructureProteinPrediction>();
+		int c = 0;
+		for (Row r : rows) {
+			StructureProteinPrediction structure = new StructureProteinPrediction(queryProtein, r.getString("JobID"), r.getMap(
+					"Predictions", String.class, String.class));
+			res.add(structure);
+			++c;
+		}
+		final long endTime = System.currentTimeMillis();
+		System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
+		return res;
+	}
+
+	/*
+	 * getting part of protein sequence from the db ProteinRow
+	 */
+	public List<StructureProteinPrediction> ReadPartOfSequence(String queryProtein) {
+		final long startTime = System.currentTimeMillis();
+		String com = "SELECT * FROM ProteinRow;";
+		System.out.println("Command: " + com);
+		ResultSet results = session.execute(com);
+		if (results.isExhausted())
+			return null;
+		final long queryTime = System.currentTimeMillis();
+		List<Row> rows = results.all();
+		System.out.println("Query time is " + (queryTime - startTime) + " msec");
+		System.out.println(" rows analysed,  " + rows.size());
+		List<StructureProteinPrediction> res = new ArrayList<StructureProteinPrediction>();
+		int c = 0;
+		for (Row r : rows) {
+			String prot = r.getString("Protein");
+			if (prot.matches("(.*)" + queryProtein + "(.*)")) {
+				StructureProteinPrediction structure = new StructureProteinPrediction(prot, r.getString("JobID"), r.getMap("Predictions",
+						String.class, String.class));
+				res.add(structure);
+				++c;
+			}
+		}
+		final long endTime = System.currentTimeMillis();
+		System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
+		return res;
+	}
+
+	/*
+	 * getting protein sequences by counter
+	 */
+	public Map<String, Integer> ReadProteinSequenceByCounter() {
+		final long startTime = System.currentTimeMillis();
+		String com = "SELECT Protein FROM ProteinRow;";
+		System.out.println("Command: " + com);
+		ResultSet results = session.execute(com);
+		if (results.isExhausted())
+			return null;
+		final long queryTime = System.currentTimeMillis();
+		List<Row> rows = results.all();
+		System.out.println("Query time is " + (queryTime - startTime) + " msec");
+		System.out.println(" rows analysed,  " + rows.size());
+		Map<String, Integer> res = new HashMap<String, Integer>();
+		int c = 0;
+		for (Row r : rows) {
+			String protein = r.getString("Protein");
+			if (res.containsKey(protein))
+				res.put(protein, res.get(protein) + 1);
+			else
+				res.put(protein, 1);
+		}
+		final long endTime = System.currentTimeMillis();
+		System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
+		return res;
+	}
+
+	/*
+	 * getting protein sequences by counter
+	 */
+	public StructureJobLog ReadJobLog(String jobid) {
+		final long startTime = System.currentTimeMillis();
+		String com = "SELECT * FROM ProteinLog WHERE JobID = '" + jobid + "';";
+		System.out.println("Command: " + com);
+		ResultSet results = session.execute(com);
+		if (results.isExhausted())
+			return null;
+		final long queryTime = System.currentTimeMillis();
+		Row row = results.one();
+		String com1 = "SELECT * FROM ProteinRow WHERE JobID = '" + jobid + "' ALLOW FILTERING;";
+		System.out.println("Command: " + com1);
+		ResultSet results1 = session.execute(com1);
+		if (results1.isExhausted())
+			return null;
+		Row row1 = results1.one();
+		StructureJobLog res = new StructureJobLog(row.getString("Protein"), row.getString("JobID"), row.getString("DataBegin"),
+				row.getString("DataEnd"), row.getString("ip"), row1.getMap("Predictions", String.class, String.class));
+		System.out.println("Query time is " + (queryTime - startTime) + " msec");
+		final long endTime = System.currentTimeMillis();
+		System.out.println(" rows analysed, execution time is " + (endTime - startTime) + " msec");
+		return res;
+	}
+}
diff --git a/src/main/java/compbio/cassandra/CassandraWriter.java b/src/main/java/compbio/cassandra/CassandraWriter.java
new file mode 100644
index 0000000..48bbda7
--- /dev/null
+++ b/src/main/java/compbio/cassandra/CassandraWriter.java
@@ -0,0 +1,144 @@
+package compbio.cassandra;
+
+import java.util.List;
+
+import org.apache.log4j.Logger;
+
+import com.datastax.driver.core.Row;
+import com.datastax.driver.core.Session;
+import com.datastax.driver.core.ResultSet;
+
+import compbio.engine.JpredJob;
+import compbio.engine.ProteoCachePropertyHelperManager;
+import compbio.util.PropertyHelper;
+
+public class CassandraWriter {
+	private Session session;
+	private static final PropertyHelper ph = ProteoCachePropertyHelperManager.getPropertyHelper();
+	private static Logger log = Logger.getLogger(CassandraNativeConnector.class);
+
+	CassandraWriter() {
+		Session inis = CassandraNativeConnector.getSession();
+		setSession(inis);
+	}
+
+	public void setSession(Session s) {
+		assert s != null;
+		session = s;
+	}
+
+	public boolean JobisNotInsterted(String jobid) {
+		ResultSet results1 = session.execute("SELECT * FROM ProteinLog WHERE JobID = '" + jobid + "';");
+		if (results1.isExhausted()) {
+			return true;
+		}
+		return false;
+	}
+
+	public boolean JobisNotArchived(String jobid) {
+		ResultSet results1 = session.execute("SELECT * FROM JpredArchive WHERE JobID = '" + jobid + "';");
+		if (results1.isExhausted()) {
+			return true;
+		}
+		return false;
+	}
+
+	/*
+	 * inserting data into the tables for queries
+	 */
+	public int FormQueryTables(JpredJob job) {
+		if (JobisNotInsterted(job.getJobID())) {
+			String id = job.getJobID();
+			String ip = job.getIP();
+			String protein = job.getProtein();
+			String finalstatus = job.getFinalStatus();
+			String execstatus = job.getExecutionStatus();
+			String com1 = "INSERT INTO ProteinLog " + "(JobID, IP, DataBegin, DataEnd, FinalStatus, ExecutionStatus, Protein)"
+					+ " VALUES ('" + id + "','" + ip + "','" + job.getStartingTimeStr() + "','" + job.getEndTimeStr() + "','" + finalstatus
+					+ "','" + execstatus + "','" + protein + "');";
+			session.execute(com1);
+
+			String com2 = "INSERT INTO ProteinData " + "(jobtime, JobID, Protein)" + " VALUES (" + job.getStartingDate() + ",'" + id
+					+ "','" + protein + "');";
+			session.execute(com2);
+
+			String allpredictions = "";
+			List<FastaSequence> pr = job.getPredictions();
+			for (FastaSequence pred : pr) {
+				String predictionname = pred.getId();
+				String prediction = pred.getSequence().replaceAll("\n", "");
+				allpredictions += "'" + predictionname + "':'" + prediction + "',";
+			}
+			String final_prediction = "";
+			if (!allpredictions.equals("")) {
+				final_prediction = allpredictions.substring(0, allpredictions.length() - 1);
+			}
+
+			String check2 = "SELECT * FROM ProteinRow WHERE JobID = '" + job.getJobID() + "';";
+			ResultSet results2 = session.execute(check2);
+			if (results2.isExhausted()) {
+				String com3 = "INSERT INTO ProteinRow " + "(Protein, JobID, Predictions)" + " VALUES ('" + protein + "','" + id + "',{"
+						+ final_prediction + "});";
+				session.execute(com3);
+			}
+
+			// update some internal query tables
+			String check3 = "SELECT * FROM MainParameters WHERE Name = 'EarliestJobDate';";
+			ResultSet results3 = session.execute(check3);
+			boolean updateparameter = true;
+			if (!results3.isExhausted()) {
+				Row r = results3.one();
+				if (job.getStartingDate() >= Long.parseLong(r.getString("Value")))
+					updateparameter = false;
+			}
+			if (updateparameter) {
+				String com = "INSERT INTO MainParameters " + "(Name, Value)" + " VALUES ('EarliestJobDate','" + job.getStartingDateStr()
+						+ "');";
+				session.execute(com);
+			}
+			String check4 = "SELECT * FROM JobDateInfo WHERE jobday = " + job.getStartingDate() + ";";
+			ResultSet results4 = session.execute(check4);
+			updateparameter = true;
+			int njobs = 1;
+			if (!results4.isExhausted()) {
+				Row r = results4.one();
+				njobs += r.getLong("Total");
+			}
+			String com = "INSERT INTO JobDateInfo " + "(jobday, Total)" + " VALUES (" + job.getStartingDate() + "," + njobs + ");";
+			session.execute(com);
+
+			return 1;
+		}
+		return 0;
+	}
+
+	/*
+	 * insert data from a real Jpred job: timing+IP, Execution Status, Final
+	 * status, protein sequence, predictions, alignment, LOG and tar.gz files
+	 */
+	public int ArchiveData(JpredJob job, String archivepath) {
+		if (JobisNotArchived(job.getJobID())) {
+			String id = job.getJobID();
+			String log = job.getLog().replaceAll("'", "");
+			String com = "INSERT INTO JpredArchive (JobID, Protein, IP, StartTime, ExecTime,LOG, ArchiveLink) VALUES ('" + id + "','"
+					+ job.getProtein() + "','" + job.getIP() + "'," + job.getStartingTime() + "," + job.getExecutionTime() + ",'" + log
+					+ "','" + archivepath + "');";
+			session.execute(com);
+
+			List<FastaSequence> predictions = job.getPredictions();
+			for (FastaSequence p : predictions) {
+				session.execute("UPDATE JpredArchive SET predictions = predictions + {'" + p.getId() + "':'"
+						+ p.getSequence().replaceAll("\n", "") + "'} WHERE JobID = '" + id + "';");
+			}
+
+			List<FastaSequence> seqs = job.getAlignment();
+			for (FastaSequence s : seqs) {
+				session.execute("UPDATE JpredArchive SET alignment = alignment + {'" + s.getId() + "':'"
+						+ s.getSequence().replaceAll("\n", "") + "'} WHERE JobID = '" + id + "';");
+			}
+			return 1;
+		}
+		return 0;
+	}
+
+}
diff --git a/src/main/java/compbio/cassandra/DataBase.java b/src/main/java/compbio/cassandra/DataBase.java
new file mode 100644
index 0000000..91eabf0
--- /dev/null
+++ b/src/main/java/compbio/cassandra/DataBase.java
@@ -0,0 +1,117 @@
+package compbio.cassandra;
+
+import java.util.List;
+import java.util.ArrayList;
+import java.util.Collections;
+
+public class DataBase {
+	private String date;
+	private int total;
+	private int totalJobs;
+	private int totalId;
+	private String id;
+	private String prot;
+	private String jpred;
+	private List<String> subProt;
+	private List<Integer> timeRez;
+	private List<Integer> timeTotalExec;
+	private StructureJobLog logInfo;
+
+	public DataBase() {
+	}
+
+	public DataBase(String dat, int total) {
+		this.date = dat;
+		this.total = total;
+	}
+
+	public void setDate(String dat) {
+		this.date = dat;
+	}
+
+	public String getDate() {
+		return date;
+	}
+
+	public void setTotal(int tot) {
+		this.total = tot;
+	}
+
+	public int getTotal() {
+		return total;
+	}
+
+	
+	public void setTotalJobs(int totalJobs) {
+		this.totalJobs = totalJobs;
+	}
+
+	public int getTotalJobs() {
+		return totalJobs;
+	}
+
+	public void setTotalId(int totId) {
+		this.totalId = totId;
+	}
+
+	public int getTotalId() {
+		return totalId;
+	}
+
+	public void setProt(String prot) {
+		this.prot = prot;
+	}
+
+	public String getProt() {
+		return prot;
+	}
+
+	public void setJpred(String jpred) {
+		this.jpred = jpred;
+	}
+
+	public String getJpred() {
+		return jpred;
+	}
+
+	public void setId(String id) {
+		this.id = id;
+	}
+
+	public String getId() {
+		return id;
+	}
+
+	public void setSubProt(List<String> subProt) {
+		this.subProt = subProt;
+	}
+
+	public List<String> getSubProt() {
+		return subProt;
+	}
+
+	public void setTimeRez(List<Integer> timeRez) {
+		this.timeRez = timeRez;
+	}
+
+	public List<Integer> getTimeRez() {
+		return timeRez;
+	}
+	
+	public void setTimeTotalExec(List<Integer> timeTotalExec) {
+		this.timeTotalExec = timeTotalExec;
+	}
+
+	public List<Integer> getTimeTotalExec() {
+		return timeTotalExec;
+	}
+	
+	public void setLogInfo(StructureJobLog logInfo){
+		this.logInfo = logInfo;
+	}
+	
+	public StructureJobLog getLogInfo() {
+		return logInfo;
+	}
+
+}
diff --git a/src/main/java/compbio/cassandra/FastaReader.java b/src/main/java/compbio/cassandra/FastaReader.java
new file mode 100644
index 0000000..4783b14
--- /dev/null
+++ b/src/main/java/compbio/cassandra/FastaReader.java
@@ -0,0 +1,173 @@
+package compbio.cassandra;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.InputStream;
+import java.util.Iterator;
+import java.util.Scanner;
+
+//import compbio.util.Util;
+
+/**
+ * Reads files with FASTA formatted sequences. All the information in the FASTA
+ * header is preserved including trailing white spaces. All the white spaces are
+ * removed from the sequence.
+ * 
+ * Examples of the correct input:
+ * 
+ * <pre>
+ * 
+ * >zedpshvyzg
+ * GCQDKNNIAELNEIMGTTRSPSDWQHMKGASPRAEIGLTGKKDSWWRHCCSKEFNKTPPPIHPDMKRWGWMWNRENFEKFLIDNFLNPPCPRLMLTKGTWWRHEDLCHEIFWSTLRWLCLGNQSFSAMIWGHLCECHRMIWWESNEHMFWLKFRRALKKMNSNGPCMGPDNREWMITNRMGKEFCGPAFAGDCQSCWRKCHKTNKICFNEKKGTPTKIDHEQKDIMDILKDIDNHRNWKQCQLWLLTSKSTDQESTTMLTWSTWRDFFIIIKQPFDHKCRGALDANGDFQIAAELKWPAPMIILRQNQKTMHDKSCHHFFTNRCPLMHTTRANDKQCSWHTRKQFICQQDFTTWQHRPDTHRILPSWCMSTRRKNHIKNTPALAFSTCEMGDLPNGWAPGTIILQRQFTQAIKLPQETTGWPRCDPKFDHWNMSKWLRQLLGRDDEMIPPQCD
+ * 
+ * >xovkactesa
+ * CPLSKWWNRRAFLSHTANHWMILMTWEGPHDGESKMRIAMMKWSPCKPTMSHFRCGLDAWAEPIRQIACESTFRM
+ * FCTTPRPIHKLTEMWGHMNGWTGAFCRQLECEWMMPPRHPHPCTSTFNNNKKRLIGQIPNEGKQLFINFQKPQHG
+ * FSESDIWIWKDNPTAWHEGLTIAGIGDGQHCWNWMPMPWSGAPTSNALIEFWTWLGMIGTRCKTQGMWWDAMNHH
+ * DQFELSANAHIAAHHMEKKMILKPDDRNLGDDTWMPPGKIWMRMFAKNTNACWPEGCRDDNEEDDCGTHNLHRMC
+ * 
+ * >ntazzewyvv
+ * CGCKIF D D NMKDNNRHG TDIKKHGFMH IRHPE KRDDC FDNHCIMPKHRRWGLWD
+ * EASINM	AQQWRSLPPSRIMKLNG	HGCDCMHSHMEAD	DTKQSGIKGTFWNG	HDAQWLCRWG	
+ * EFITEA	WWGRWGAITFFHAH	ENKNEIQECSDQNLKE	SRTTCEIID   TCHLFTRHLDGW 
+ *   RCEKCQANATHMTW ACTKSCAEQW  FCAKELMMN    
+ *   W        KQMGWRCKIFRKLFRDNCWID  FELPWWPICFCCKGLSTKSHSAHDGDQCRRW    WPDCARDWLGPGIRGEF   
+ *   FCTHICQQLQRNFWCGCFRWNIEKRMFEIFDDNMAAHWKKCMHFKFLIRIHRHGPITMKMTWCRSGCCFGKTRRLPDSSFISAFLDPKHHRDGSGMMMWSSEMRSCAIPDPQQAWNQGKWIGQIKDWNICFAWPIRENQQCWATPHEMPSGFHFILEKWDALAHPHMHIRQKKCWAWAFLSLMSSTHSDMATFQWAIPGHNIWSNWDNIICGWPRI
+ * 
+ *    > 12 d t y wi 		k	jbke  	
+ *   KLSHHDCD
+ *    N
+ *     H
+ *     HSKCTEPHCGNSHQMLHRDP
+ *     CCDQCQSWEAENWCASMRKAILF
+ * 
+ * </pre>
+ * 
+ * @author Peter Troshin
+ * @version 1.0 April 2011
+ * 
+ */
+public class FastaReader implements Iterator<FastaSequence> {
+
+	private final Scanner input;
+	/**
+	 * Delimiter for the scanner
+	 */
+	private final String DELIM = ">";
+
+	/**
+	 * Header data can contain non-ASCII symbols and read in UTF8
+	 * 
+	 * @param inputFile
+	 *            the file containing the list of FASTA formatted sequences to
+	 *            read from
+	 * @throws FileNotFoundException
+	 *             if the input file is not found
+	 * @throws IllegalStateException
+	 *             if the close method was called on this instance
+	 * 
+	 */
+	public FastaReader(final String inputFile) throws FileNotFoundException {
+		input = new Scanner(new File(inputFile), "UTF8");
+		input.useDelimiter(DELIM);
+		Runtime.getRuntime().addShutdownHook(new Thread() {
+
+			@Override
+			public void run() {
+				if (input != null) {
+					input.close();
+				}
+			}
+		});
+	}
+
+	/**
+	 * This class will not close the incoming stream! So the client should do
+	 * so.
+	 * 
+	 * @param inputStream
+	 * @throws FileNotFoundException
+	 */
+	public FastaReader(final InputStream inputStream)
+			throws FileNotFoundException {
+		input = new Scanner(inputStream);
+		input.useDelimiter(DELIM);
+	}
+
+	/**
+	 * {@inheritDoc}
+	 * 
+	 * @throws IllegalStateException
+	 *             if the close method was called on this instance
+	 */
+	@Override
+	public boolean hasNext() {
+		return input.hasNext();
+	}
+
+	/**
+	 * Reads the next FastaSequence from the input
+	 * 
+	 * @throws AssertionError
+	 *             if the header or the sequence is missing
+	 * @throws IllegalStateException
+	 *             if the close method was called on this instance
+	 * @throws MismatchException
+	 *             - if there were no more FastaSequence's.
+	 */
+	@Override
+	public FastaSequence next() {
+		String fastaHeader = input.next();
+		while (fastaHeader.indexOf("\n") < 0 && input.hasNext()) {
+			fastaHeader = fastaHeader.concat(">");
+			fastaHeader = fastaHeader.concat(input.next());
+		}
+		return FastaReader.toFastaSequence(fastaHeader);
+	}
+
+	/**
+	 * Not implemented
+	 */
+	@Override
+	public void remove() {
+		throw new UnsupportedOperationException();
+	}
+
+	/**
+	 * Call this method to close the connection to the input file if you want to
+	 * free up the resources. The connection will be closed on the JVM shutdown
+	 * if this method was not called explicitly. No further reading on this
+	 * instance of the FastaReader will be possible after calling this method.
+	 */
+	public void close() {
+		input.close();
+	}
+
+	private static FastaSequence toFastaSequence(final String singleFastaEntry) {
+
+		// assert !Util.isEmpty(singleFastaEntry) :
+		// "Empty String where FASTA sequence is expected!";
+
+		int nlineidx = singleFastaEntry.indexOf("\n");
+		if (nlineidx < 0) {
+			throw new AssertionError(
+					"The FASTA sequence must contain the header information"
+							+ " separated by the new line from the sequence. Given sequence does not appear to "
+							+ "contain the header! Given data:\n "
+							+ singleFastaEntry);
+		}
+		String header = singleFastaEntry.substring(0, nlineidx);
+
+		// Get rid of the new line chars (should cover common cases)
+		header = header.replaceAll("\r", "");
+
+		String sequence = singleFastaEntry.substring(nlineidx);
+
+		/*
+		 * if (Util.isEmpty(sequence)) { throw new AssertionError(
+		 * "Empty sequences are not allowed! Please make sure the " +
+		 * " data is in the FASTA format! Given data:\n " + singleFastaEntry); }
+		 */
+		return new FastaSequence(header, sequence);
+	}
+}
diff --git a/src/main/java/compbio/cassandra/FastaSequence.java b/src/main/java/compbio/cassandra/FastaSequence.java
new file mode 100644
index 0000000..61f49c7
--- /dev/null
+++ b/src/main/java/compbio/cassandra/FastaSequence.java
@@ -0,0 +1,179 @@
+package compbio.cassandra;
+
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+
+//import compbio.util.SysPrefs;
+//import compbio.util.annotation.Immutable;
+
+/**
+ * A FASTA formatted sequence. Please note that this class does not make any
+ * assumptions as to what sequence it stores e.g. it could be nucleotide,
+ * protein or even gapped alignment sequence! The only guarantee it makes is
+ * that the sequence does not contain white space characters e.g. spaces, new
+ * lines etc
+ * 
+ * @author pvtroshin
+ * 
+ * @version 1.0 September 2009
+ */
+
+@XmlAccessorType(XmlAccessType.FIELD)
+//@Immutable
+public class FastaSequence {
+
+	/**
+	 * Sequence id
+	 */
+	private String id;
+
+	// TODO what about gapped sequence here! should be indicated
+	/**
+	 * Returns the string representation of sequence
+	 */
+	private String sequence;
+
+	FastaSequence() {
+		// Default constructor for JaxB
+	}
+
+	/**
+	 * Upon construction the any whitespace characters are removed from the
+	 * sequence
+	 * 
+	 * @param id
+	 * @param sequence
+	 */
+	public FastaSequence(String id, String sequence) {
+		this.id = id;
+		this.sequence = sequence;
+	}
+
+	/**
+	 * Gets the value of id
+	 * 
+	 * @return the value of id
+	 */
+	public String getId() {
+		return this.id;
+	}
+
+	/**
+	 * Gets the value of sequence
+	 * 
+	 * @return the value of sequence
+	 */
+	public String getSequence() {
+		return this.sequence;
+	}
+
+	public static int countMatchesInSequence(final String theString,
+			final String theRegExp) {
+		final Pattern p = Pattern.compile(theRegExp);
+		final Matcher m = p.matcher(theString);
+		int cnt = 0;
+		while (m.find()) {
+			cnt++;
+		}
+		return cnt;
+	}
+
+	public String getFormattedFasta() {
+		return getFormatedSequence(80);
+	}
+
+	/**
+	 * 
+	 * @return one line name, next line sequence, no matter what the sequence
+	 *         length is
+	 */
+/*	public String getOnelineFasta() {
+		String fasta = ">" + getId() + SysPrefs.newlinechar;
+		fasta += getSequence() + SysPrefs.newlinechar;
+		return fasta;
+	}
+
+	/**
+	 * Format sequence per width letter in one string. Without spaces.
+	 * 
+	 * @return multiple line formated sequence, one line width letters length
+	 * 
+	 */
+	public String getFormatedSequence(final int width) {
+		if (sequence == null) {
+			return "";
+		}
+
+		assert width >= 0 : "Wrong width parameter ";
+
+		final StringBuilder sb = new StringBuilder(sequence);
+		// int tail = nrOfWindows % WIN_SIZE;
+		// final int turns = (nrOfWindows - tail) / WIN_SIZE;
+
+		int tailLen = sequence.length() % width;
+		// add up inserted new line chars
+		int nchunks = (sequence.length() - tailLen) / width;
+		int nlineCharcounter = 0;
+		int insPos = 0;
+		for (int i = 1; i <= nchunks; i++) {
+			insPos = width * i + nlineCharcounter;
+			// to prevent inserting new line in the very end of a sequence then
+			// it would have failed.
+			if (sb.length() <= insPos) {
+				break;
+			}
+			sb.insert(insPos, "\n");
+			nlineCharcounter++;
+		}
+		// sb.insert(insPos + tailLen, "\n");
+		return sb.toString();
+	}
+
+	/**
+	 * 
+	 * @return sequence length
+	 */
+	public int getLength() {
+		return this.sequence.length();
+	}
+
+	/**
+	 * Same as oneLineFasta
+	 */
+//	@Override
+//	public String toString() {
+//		return this.getOnelineFasta();
+	// }
+
+	@Override
+	public int hashCode() {
+		final int prime = 17;
+		int result = 1;
+		result = prime * result + ((id == null) ? 0 : id.hashCode());
+		result = prime * result
+				+ ((sequence == null) ? 0 : sequence.hashCode());
+		return result;
+	}
+
+	@Override
+	public boolean equals(Object obj) {
+		if (obj == null) {
+			return false;
+		}
+		if (!(obj instanceof FastaSequence)) {
+			return false;
+		}
+		FastaSequence fs = (FastaSequence) obj;
+		if (!fs.getId().equals(this.getId())) {
+			return false;
+		}
+		if (!fs.getSequence().equalsIgnoreCase(this.getSequence())) {
+			return false;
+		}
+		return true;
+	}
+
+}
diff --git a/src/main/java/compbio/cassandra/JpredParser.java b/src/main/java/compbio/cassandra/JpredParser.java
new file mode 100644
index 0000000..27020ec
--- /dev/null
+++ b/src/main/java/compbio/cassandra/JpredParser.java
@@ -0,0 +1,16 @@
+package compbio.cassandra;
+
+import java.io.IOException;
+
+public interface JpredParser {
+
+	/*
+	 * Defines a source file with metainformation of Jpred Jobs
+	 **/
+	void setSource (String newsourceprefix);
+	
+	/*
+	 * Makes real parsing of the source file
+	 **/
+	void Parsing(String source, int nDays) throws IOException;
+}
diff --git a/src/main/java/compbio/cassandra/JpredParserHTTP.java b/src/main/java/compbio/cassandra/JpredParserHTTP.java
new file mode 100644
index 0000000..e53ddd8
--- /dev/null
+++ b/src/main/java/compbio/cassandra/JpredParserHTTP.java
@@ -0,0 +1,205 @@
+package compbio.cassandra;
+
+import java.io.BufferedReader;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.net.HttpURLConnection;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.net.URLConnection;
+import java.util.ArrayList;
+import java.util.Calendar;
+import java.util.Date;
+import java.util.List;
+
+import compbio.cassandra.JpredParser;
+import compbio.engine.JpredJob;
+
+public class JpredParserHTTP implements JpredParser {
+	private CassandraWriter cw = new CassandraWriter();
+	private String dirprefix;
+	private List<FastaSequence> alignment;
+	private List<FastaSequence> predictions;
+	private int countNoData;
+
+	public JpredParserHTTP() {
+		dirprefix = "http://www.compbio.dundee.ac.uk/www-jpred/results";
+	}
+
+	public JpredParserHTTP(String sourceurl) {
+		dirprefix = sourceurl;
+	}
+
+	public void setSource(String newsourceprefix) {
+		dirprefix = newsourceprefix;
+	}
+
+	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) {
+			cal.add(Calendar.DATE, 1);
+			String date = cal.get(Calendar.YEAR) + "/" + (cal.get(Calendar.MONTH) + 1) + "/" + cal.get(Calendar.DATE);
+			ParsingForDate(source, date);
+		}
+	}
+
+	/*
+	 * The method parses the Jpred output concise file in the FASTA format If
+	 * there is a record with ID = QUERY or jobid, this a "one protein" job
+	 * otherwise this is an alignment job
+	 */
+	private String parsePredictions(final InputStream stream, String jobid) throws FileNotFoundException {
+		final FastaReader fr = new FastaReader(stream);
+		String protein = "";
+		alignment = new ArrayList<FastaSequence>();
+		predictions = new ArrayList<FastaSequence>();
+		while (fr.hasNext()) {
+			final FastaSequence fs = fr.next();
+			String seqid = fs.getId();
+			String seq = fs.getSequence().replaceAll("\n", "");
+			if (seqid.equals("jnetpred") || seqid.equals("Lupas_21") || seqid.equals("Lupas_14") || seqid.equals("Lupas_28")
+					|| seqid.equals("JNETSOL25") || seqid.equals("JNETSOL5") || seqid.equals("JNETSOL0") || seqid.equals("JNETCONF")
+					|| seqid.equals("JNETHMM") || seqid.equals("JNETPSSM") || seqid.equals("JNETCONF")) {
+				predictions.add(fs);
+			} else {
+				alignment.add(fs);
+				if (seqid.equals("QUERY") || seqid.equals(jobid))
+					protein = seq;
+			}
+		}
+		return protein;
+	}
+
+	private String parseLogFile(final InputStream stream) throws IOException {
+		String out = "";
+		BufferedReader buffer = new BufferedReader(new InputStreamReader(stream));
+		String line;
+		while (null != (line = buffer.readLine())) {
+			out += line;
+		}
+		return out;
+	}
+
+	private int analyseJob(String[] jobinfo) throws IOException {
+		boolean running = true;
+		boolean ConcisefileExists = false;
+		boolean LogfileExists = false;
+		JpredJob job = new JpredJob (jobinfo[jobinfo.length - 1], jobinfo[0], jobinfo[1]);
+		job.setIP(jobinfo[2]);
+		Date currDate = new Date();
+		String maindir = dirprefix + "/" + job.getJobID() + "/";
+
+		//System.out.println("analyzing job " + job.getJobID());
+		try {
+			URL dirurl = new URL(maindir);
+			HttpURLConnection httpConnection_dirurl = (HttpURLConnection) dirurl.openConnection();
+			if (httpConnection_dirurl.getResponseCode() < 199 || 300 <= httpConnection_dirurl.getResponseCode()) {
+				return 0;
+			}
+			URL conciseurl = new URL(maindir + job.getJobID() + ".concise.fasta");
+			URL archiveurl = new URL(maindir + job.getJobID() + ".tar.gz");
+			URL logurl = new URL(maindir + "LOG");
+			HttpURLConnection httpConnection_conciseurl = (HttpURLConnection) conciseurl.openConnection();
+			HttpURLConnection httpConnection_logurl = (HttpURLConnection) logurl.openConnection();
+			HttpURLConnection httpConnection_archiveurl = (HttpURLConnection) archiveurl.openConnection();
+			if (199 < httpConnection_conciseurl.getResponseCode() && httpConnection_conciseurl.getResponseCode() < 300) {
+				ConcisefileExists = true;
+				running = false;
+				try {
+					job.setProtein(parsePredictions(conciseurl.openStream(), job.getJobID()));
+				} catch (IOException e) {
+					e.printStackTrace();
+				}
+			} else {
+				// The job still can be running of failed...
+				++countNoData;
+			}
+			if (199 < httpConnection_logurl.getResponseCode() && httpConnection_logurl.getResponseCode() < 300) {
+				LogfileExists = true;
+				job.setLog(parseLogFile(logurl.openStream()));
+			} else {
+				// The job has not been started at all...
+				job.setExecutionStatus("FAIL");
+				job.setFinalStatus("STOPPED");
+				running = false;
+			}
+			if (job.getLog().matches("(.*)TIMEOUT\\syour\\sjob\\stimed\\sout(.*)")) {
+				// blast job was too long (more than 3600 secs by default)...
+				job.setExecutionStatus("FAIL");
+				job.setFinalStatus("TIMEDOUT");
+				running = false;
+			} else if (job.getLog().matches("(.*)Jpred\\serror:\\sDied\\sat(.*)")) {
+				// an internal Jpred error...
+				job.setExecutionStatus("FAIL");
+				job.setFinalStatus("JPREDERROR");
+				running = false;
+			} else if ((currDate.getTime() - job.getEndTime()) / 1000 > 3601 && LogfileExists && !ConcisefileExists) {
+				// the job was stopped with unknown reason...
+				job.setExecutionStatus("FAIL");
+				job.setFinalStatus("STOPPED");
+				running = false;
+			}
+
+			httpConnection_conciseurl.disconnect();
+			httpConnection_logurl.disconnect();
+			httpConnection_archiveurl.disconnect();
+		} catch (MalformedURLException e) {
+			e.printStackTrace();
+		}
+
+		if (!running) {
+			job.setAlignment(alignment);
+			job.setPredictions(predictions);
+			cw.FormQueryTables(job);
+			cw.ArchiveData(job, "undefined");
+			return 1;
+		}
+
+		return 0;
+	}
+
+	private void ParsingForDate(String input, String date) {
+		int totalcount = 0;
+		int countinsertions = 0;
+		int countinserted = 0;
+		int countNotanalyzed = 0;
+		countNoData = 0;
+
+		System.out.println("Inserting jobs for " + date);
+		try {
+			URL url = new URL(input);
+			URLConnection conn = url.openConnection();
+			BufferedReader alljobs = new BufferedReader(new InputStreamReader(conn.getInputStream()));
+			String line;
+
+			while ((line = alljobs.readLine()) != null) {
+				if (line.matches(date + ":(.*)jp_[^\\s]+")) {
+					totalcount++;
+					String[] job = line.split("\\s+");
+					String jobid = job[job.length - 1];
+					if (cw.JobisNotInsterted(jobid)) {
+						countinsertions += analyseJob(job);
+					} else {
+						++countinserted;
+					}
+				} else {
+					++countNotanalyzed;
+				}
+			}
+			alljobs.close();
+			System.out.println("Total number of jobs = " + totalcount);
+			System.out.println("   " + countinserted + " jobs inserted already");
+			System.out.println("   " + countNotanalyzed + " not analysed jobs");
+			System.out.println("   " + countNoData + " jobs without *.concise.fasta file (RUNNING or FAILED)");
+			System.out.println("   " + countinsertions + " new job insertions\n");
+		} catch (MalformedURLException e) {
+			e.printStackTrace();
+		} catch (IOException e) {
+			e.printStackTrace();
+		}
+		;
+	}
+}
diff --git a/src/main/java/compbio/cassandra/JpredParserLocalFile.java b/src/main/java/compbio/cassandra/JpredParserLocalFile.java
new file mode 100644
index 0000000..d4a22e6
--- /dev/null
+++ b/src/main/java/compbio/cassandra/JpredParserLocalFile.java
@@ -0,0 +1,134 @@
+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;
+import java.util.ArrayList;
+import java.util.Calendar;
+import java.util.Date;
+import java.util.List;
+
+public class JpredParserLocalFile implements JpredParser {
+	private CassandraWriter cw = new CassandraWriter();
+	private String dirprefix;
+
+	public void setSource(String newsourceprefix) {
+		this.dirprefix = newsourceprefix;
+	}
+
+	public JpredParserLocalFile() {
+		this.dirprefix = "/home/asherstnev/Projects/Java.projects/proteocache/data_stress_test/data.dat";
+	}
+
+	public JpredParserLocalFile(String sourceurl) {
+		this.dirprefix = sourceurl;
+	}
+
+	public void Parsing(String source, int nDays) throws IOException {
+		Calendar cal = Calendar.getInstance();
+		cal.add(Calendar.DATE, -nDays);
+		List<String> alljobs = new ArrayList<String>();
+		File file = new File(source);
+		BufferedReader alljobsfile = new BufferedReader(new InputStreamReader(new FileInputStream(file)));
+		String line;
+
+		while ((line = alljobsfile.readLine()) != null) {
+			alljobs.add(line);
+		}
+		alljobsfile.close();
+
+		System.out.println("Inserting jobs for " + nDays + " days, " + alljobs.size() + " jobs in total");
+		final long startTime = System.currentTimeMillis();
+		for (int i = 0; i < nDays; ++i) {
+			cal.add(Calendar.DATE, 1);
+			int month = cal.get(Calendar.MONTH) + 1;
+			int year = cal.get(Calendar.YEAR);
+			int day = cal.get(Calendar.DATE);
+			String date = year + "/" + month + "/" + day;
+			ParsingForDate(alljobs, date);
+		}
+		final long execTime = System.currentTimeMillis() - startTime;
+		System.out.println("Execution Time = " + execTime + " ms");
+	}
+
+	private void ParsingForDate(List<String> input, String date) {
+		int totalcount = 0;
+		int countNoData = 0;
+		int countUnclearFASTAid = 0;
+		int countinsertions = 0;
+		int countinserted = 0;
+		int counAlignments = 0;
+		int countStrange = 0;
+
+		System.out.println("Inserting jobs for " + date);
+		for (String in : input) {
+			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";
+				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 insertdate = 0;
+							try {
+								Date dat = formatter.parse(dateInString1);
+								insertdate = dat.getTime();
+							} catch (ParseException e) {
+								e.printStackTrace();
+							}
+							//countinsertions += cw.FormQueryTables(insertdate, starttime, finishtime, ip, id, "OK", "OK", newprotein, seqs);
+						}
+						fr.close();
+					} catch (IOException e) {
+						e.printStackTrace();
+					}
+				} else {
+					countNoData++;
+				}
+			} else {
+				if (in.matches(date + "(.*)Sequence0/(.*)")) {
+					++counAlignments;
+				} else {
+					++countStrange;
+				}
+			}
+		}
+		if (true) {
+			System.out.println("Total number of jobs = " + totalcount);
+			System.out.println("   " + countinserted + " jobs inserted already");
+			System.out.println("   " + counAlignments + " jalview jobs");
+			System.out.println("   " + countStrange + " not analysed jobs");
+			System.out.println("   " + countNoData + " jobs without *.concise.fasta file");
+			System.out.println("   " + countUnclearFASTAid + " jobs with unclear FASTA protein id in *.concise.fasta");
+			System.out.println("   " + countinsertions + " new job insertions\n");
+		}
+	}
+
+}
diff --git a/src/main/java/compbio/cassandra/Pair.java b/src/main/java/compbio/cassandra/Pair.java
new file mode 100644
index 0000000..d942fea
--- /dev/null
+++ b/src/main/java/compbio/cassandra/Pair.java
@@ -0,0 +1,24 @@
+package compbio.cassandra;
+
+public class Pair<K, V> {
+
+	private final K element0;
+	private final V element1;
+
+	public static <K, V> Pair<K, V> createPair(K element0, V element1) {
+		return new Pair<K, V>(element0, element1);
+	}
+
+	public Pair(K element0, V element1) {
+		this.element0 = element0;
+		this.element1 = element1;
+	}
+
+	public K getElement0() {
+		return element0;
+	}
+
+	public V getElement1() {
+		return element1;
+	}
+}
\ No newline at end of file
diff --git a/src/main/java/compbio/cassandra/StructureJobLog.java b/src/main/java/compbio/cassandra/StructureJobLog.java
new file mode 100644
index 0000000..b2d0400
--- /dev/null
+++ b/src/main/java/compbio/cassandra/StructureJobLog.java
@@ -0,0 +1,45 @@
+package compbio.cassandra;
+
+import java.util.Map;
+
+public class StructureJobLog {
+	private String jobid;
+	private String dateStart;
+	private String dateEnd;
+	private String sequence;
+	private String ip;	
+	private Map<String,String> prediction;
+	
+	public StructureJobLog (String seq, String id, String  dateStart, String  dateEnd, String ip, Map<String,String> pred) {
+		this.sequence = seq;
+		this.jobid = id;
+		this.dateStart = dateStart;
+		this.dateEnd = dateEnd;
+		this.ip = ip;
+		this.prediction = pred;
+	}
+	
+	public String getSequence () {
+		return sequence;
+	}
+	
+	public String getJobid () {
+		return jobid;
+	}
+	
+	public String getDateStart () {
+		return dateStart;
+	}
+	
+	public String getDateEnd () {
+		return dateEnd;
+	}
+	
+	public String getIp () {
+		return ip;
+	}
+	
+	public Map<String,String> getPrediction () {
+		return prediction;
+	}
+}
diff --git a/src/main/java/compbio/cassandra/StructureProteinPrediction.java b/src/main/java/compbio/cassandra/StructureProteinPrediction.java
new file mode 100644
index 0000000..936a67a
--- /dev/null
+++ b/src/main/java/compbio/cassandra/StructureProteinPrediction.java
@@ -0,0 +1,28 @@
+package compbio.cassandra;
+
+import java.util.Map;
+
+public class StructureProteinPrediction {
+	private String sequence;
+	private String jobid;
+	private Map<String,String> prediction;
+	
+	public StructureProteinPrediction (String seq, String id, Map<String,String> pred) {
+		this.sequence = seq;
+		this.jobid = id;
+		this.prediction = pred;
+	}
+	
+	public String getSequence () {
+		return sequence;
+	}
+	
+	public String getJobid () {
+		return jobid;
+	}
+	
+	public Map<String,String> getPrediction () {
+		return prediction;
+	}
+
+}
diff --git a/src/main/java/compbio/cassandra/readers/CassandraReaderExecutionTime.java b/src/main/java/compbio/cassandra/readers/CassandraReaderExecutionTime.java
new file mode 100644
index 0000000..347ebe3
--- /dev/null
+++ b/src/main/java/compbio/cassandra/readers/CassandraReaderExecutionTime.java
@@ -0,0 +1,104 @@
+package compbio.cassandra.readers;
+
+
+import java.util.Calendar;
+import java.util.List;
+import java.util.ArrayList;
+
+import org.apache.log4j.Logger;
+
+import com.datastax.driver.core.Row;
+import com.datastax.driver.core.Session;
+import com.datastax.driver.core.ResultSet;
+import com.datastax.driver.core.PreparedStatement;
+import com.datastax.driver.core.BoundStatement;
+
+import compbio.cassandra.CassandraReader;
+import compbio.cassandra.Pair;
+import compbio.engine.ProteoCachePropertyHelperManager;
+import compbio.util.PropertyHelper;
+
+public class CassandraReaderExecutionTime {
+	private Session session;
+
+	public static String CASSANDRA_HOSTNAME = "localhost";
+	public static boolean READ_WEB_JPRED = false;
+	public static boolean READ_LOCALFILE_JPRED = false;
+
+	public void setSession(Session s) {
+		assert s != null;
+		session = s;
+	}
+
+	private void setConditions() {
+
+	}
+
+	public boolean JobisNotInsterted(String jobid) {
+		ResultSet results1 = session.execute("SELECT * FROM ProteinLog WHERE JobID = '" + jobid + "';");
+		if (results1.isExhausted()) {
+			return true;
+		}
+		return false;
+	}
+
+	public boolean JobisNotArchived(String jobid) {
+		ResultSet results1 = session.execute("SELECT * FROM JpredArchive WHERE JobID = '" + jobid + "';");
+		if (results1.isExhausted()) {
+			return true;
+		}
+		return false;
+	}
+
+	/*
+	 * getting data from the db
+	 */
+	public List<Pair<String, String>> ReadProteinDataTable() {
+		final long startTime = System.currentTimeMillis();
+		String com = "SELECT DataBegin,DataEnd FROM ProteinKeyspace.ProteinLog;";
+		System.out.println("Command: " + com);
+		ResultSet results = session.execute(com);
+		final long queryTime = System.currentTimeMillis();
+		List<Row> rows = results.all();
+		System.out.println("Query time is " + (queryTime - startTime) + " msec");
+
+		List<Pair<String, String>> res = new ArrayList<Pair<String, String>>();
+		int c = 0;
+		for (Row r : rows) {
+			Pair<String, String> pair = new Pair<String, String>(r.getString("DataBegin"), r.getString("DataEnd"));
+			res.add(pair);
+			++c;
+		}
+		final long endTime = System.currentTimeMillis();
+		System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
+		return res;
+	}
+
+	/*
+	 * getting earlest date of jobs from the db
+	 */
+	public long getEarliestDateInDB() {
+		final long startTime = System.currentTimeMillis();
+		String com = "SELECT jobtime FROM ProteinKeyspace.ProteinData;";
+		System.out.println("Command: " + com);
+		ResultSet results = session.execute(com);
+		final long queryTime = System.currentTimeMillis();
+		System.out.println("Query time is " + (queryTime - startTime) + " msec");
+
+		Calendar cal = Calendar.getInstance();
+		long res = cal.getTimeInMillis();
+		int c = 0;
+		while (!results.isExhausted()) {
+			Row r = results.one();
+			long d1 = r.getLong("jobtime");
+			if (res > d1) {
+				res = d1;
+			}
+			++c;
+		}
+		final long endTime = System.currentTimeMillis();
+		System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
+		return res;
+	}
+
+}
diff --git a/src/main/java/compbio/engine/Job.java b/src/main/java/compbio/engine/Job.java
new file mode 100644
index 0000000..309e0e9
--- /dev/null
+++ b/src/main/java/compbio/engine/Job.java
@@ -0,0 +1,167 @@
+package compbio.engine;
+
+import java.text.ParseException;
+import java.text.SimpleDateFormat;
+import java.util.Date;
+
+public class Job {
+	private String jobid;
+	private String ExecutionStatus;
+	private String FinalStatus;
+	private String IP;
+	private String Email;
+
+	private String StartingDateStr;
+	private long StartingDate;
+	private String EndTimeStr;
+	private long EndTime;
+	private String StartingTimeStr;
+	private long StartingTime;
+	private long ExecutionTime;
+
+	static SimpleDateFormat dateformatter =  new SimpleDateFormat("yyyy/MM/dd");;
+	static SimpleDateFormat timeformatter = new SimpleDateFormat("yyyy/MM/dd:H:m:s");
+
+	public Job() {
+		ExecutionStatus = "OK";
+		FinalStatus = "OK";
+		jobid = "";
+		
+		StartingDateStr = "1970/1/1";
+		StartingTimeStr = "1970/1/1:0:0:0";
+		EndTimeStr = "1970/1/1:0:0:0";
+		StartingDate = 0L;
+		StartingTime = 0L;
+		EndTime = 0L;
+		ExecutionTime = 0L;
+	}
+
+	public Job(String id, String date1, String date2) {
+		jobid = id;
+		ExecutionStatus = "OK";
+		FinalStatus = "OK";
+		setDates(date1, date2);
+	}
+
+	protected void setDates (String d1, String d2) {
+		StartingTimeStr = d1;
+		StartingDateStr = d1.substring(0, d1.indexOf(":"));
+		StartingTime = convertTime(StartingTimeStr);
+		StartingDate = convertDate(StartingDateStr);
+
+		EndTimeStr = d2;
+		EndTime = convertTime(d2);
+		ExecutionTime = EndTime - StartingTime;
+	}
+	
+	
+	protected long convertDate (String d) {
+		try {
+			if (null != d) {
+				Date startdate = dateformatter.parse(d);
+				return startdate.getTime();
+			}
+		} catch (ParseException e) {
+			e.printStackTrace();
+		}
+		return 0L;
+	}
+	
+	protected long convertTime (String d) {
+		try {
+			if (null != d) {
+				Date startdate = timeformatter.parse(d);
+				return startdate.getTime();
+			}
+		} catch (ParseException e) {
+			e.printStackTrace();
+		}
+		return 0L;
+	}
+	
+	
+	public void setStartingDate(String date) {
+		this.StartingDateStr = date;
+		StartingDate = convertDate(date);
+		StartingTime = convertTime(date);
+		if (0 < EndTime) {
+			ExecutionTime = EndTime - StartingTime;
+		}
+	}
+
+	public void setEndTime(String date) {
+		this.EndTimeStr = date;
+		EndTime = convertTime(date);
+		if (0 < StartingTime) {
+			ExecutionTime = EndTime - StartingTime;
+		}
+	}
+
+	public String getStartingDateStr() {
+		return StartingDateStr;
+	}
+	public String getStartingTimeStr() {
+		return StartingTimeStr;
+	}
+	public long getStartingDate() {
+		return StartingDate;
+	}
+	public long getStartingTime() {
+		return StartingTime;
+	}
+
+	public String getEndTimeStr() {
+		return EndTimeStr;
+	}
+	public long getEndTime() {
+		return EndTime;
+	}
+
+	public void setExecutionStatus(String status) {
+		ExecutionStatus = status;
+	}
+
+	public void setFinalStatus(String status) {
+		FinalStatus = status;
+	}
+	
+	public String getExecutionStatus() {
+		return ExecutionStatus;
+	}
+
+	public String getFinalStatus() {
+		return FinalStatus;
+	}
+
+	public long getExecutionTime() {
+		return ExecutionTime;
+	}
+	
+	public void setIP(String IP) {
+		this.IP = IP;
+	}
+
+	public String getIP() {
+		if (null != IP)
+			return IP;
+		return "127.0.0.1";
+	}
+	
+	public void setEmail(String email) {
+		this.Email = email;
+	}
+
+	public String getEmail() {
+		if (null != Email)
+			return Email;
+		return "user@localhost";
+	}
+
+	public void setJobId(String id) {
+		this.jobid = id;
+	}
+
+	public String getJobID() {
+		return jobid;
+	}
+}
diff --git a/src/main/java/compbio/engine/JpredJob.java b/src/main/java/compbio/engine/JpredJob.java
new file mode 100644
index 0000000..a606746
--- /dev/null
+++ b/src/main/java/compbio/engine/JpredJob.java
@@ -0,0 +1,64 @@
+package compbio.engine;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import compbio.cassandra.FastaSequence;
+
+public class JpredJob extends Job {
+	private String protein;
+	private String log;
+	private List<FastaSequence> predictions;
+	private List<FastaSequence> alignment;
+
+	public JpredJob() {
+		super();
+	}
+
+	public JpredJob(String jobid, String date1, String date2) {
+		super(jobid, date1, date2);
+		this.protein = protein;
+		predictions = new ArrayList<FastaSequence>();
+		alignment  = new ArrayList<FastaSequence>();
+		log = "";
+	}
+
+	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; 
+	}
+
+	public void setProtein(String protein) {
+		this.protein = protein;
+	}
+
+	public String getProtein() {
+		return protein;
+	}
+
+	public void setLog(String log) {
+		this.log = log;
+	}
+
+	public String getLog() {
+		return log;
+	}
+
+	public void setAlignment(List<FastaSequence> al) {
+		this.alignment = al;
+	}
+
+	public List<FastaSequence> getAlignment() {
+		return alignment;
+	}
+
+	public void setPredictions(List<FastaSequence> pr) {
+		this.predictions = pr;
+	}
+
+	public List<FastaSequence> getPredictions() {
+		return predictions;
+	}
+}
diff --git a/src/main/java/compbio/engine/ProteoCachePropertyHelperManager.java b/src/main/java/compbio/engine/ProteoCachePropertyHelperManager.java
new file mode 100644
index 0000000..4615297
--- /dev/null
+++ b/src/main/java/compbio/engine/ProteoCachePropertyHelperManager.java
@@ -0,0 +1,150 @@
+/* Copyright (c) 2009 Peter Troshin
+ *  
+ *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0     
+ * 
+ *  This library is free software; you can redistribute it and/or modify it under the terms of the
+ *  Apache License version 2 as published by the Apache Software Foundation
+ * 
+ *  This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
+ *  even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache 
+ *  License for more details.
+ * 
+ *  A copy of the license is in apache_license.txt. It is also available here:
+ * @see: http://www.apache.org/licenses/LICENSE-2.0.txt
+ * 
+ * Any republication or derived work distributed in source code form
+ * must include this copyright and license notice.
+ */
+
+package compbio.engine;
+
+import java.io.File;
+import java.io.IOException;
+import java.net.URISyntaxException;
+import java.net.URL;
+
+import org.apache.log4j.Logger;
+
+import compbio.util.PropertyHelper;
+import compbio.util.Util;
+
+public final class ProteoCachePropertyHelperManager {
+
+	private static Logger log = Logger.getLogger(ProteoCachePropertyHelperManager.class);
+	private static PropertyHelper ph = null;
+
+	/**
+	 * Ways to fix path problem: 
+	 * 1) find a path to WEB-INF directory based on the path to a known class. 
+	 * Then prepend this absolute path to the rest of paths 
+	 * pros: no input from user 
+	 * cons: relocation of the source may cause problems 
+	 * 
+	 * 2) Require users to add configuration directories to the class
+	 * path and then load entries from it. 
+	 * pros: 
+	 * cons: Many paths needs to be added. Put significant burden on the user. 
+	 * Hard to tell web appl server to add these entries to its class path. 
+	 * 
+	 * 3) Ask for project source directory explicitly in the configuration. 
+	 * pros:
+	 * cons: similar to 1, but this initial configuration file must reside in 
+	 * well known location! Why ask users what can be found automatically?
+	 * 
+	 * 4) Have everything in the location already in class path for tomcat. 
+	 * pros:
+	 * cons: only classes and lib/*.jar are added, Eclipse will remove non 
+	 * classses from classes dir.
+	 * 
+	 * Try 1 - succeed.
+	 * 
+	 * @return an instance
+	 */
+	public static PropertyHelper getPropertyHelper() {
+		if (ph == null) {
+			try {
+				File MainPropertyFile = getResourceFromClasspath("conf/Proteocache.properties");
+				ph = new PropertyHelper(MainPropertyFile);
+			} catch (IOException e) {
+				log.warn("Cannot read property files! Reason: " + e.getLocalizedMessage(), e.getCause());
+			}
+		}
+		return ph;
+	}
+
+	static File getResourceFromClasspath(String resourceName) {
+		assert !Util.isEmpty(resourceName);
+		String locPath = getLocalPath();
+		File prop = new File(locPath + resourceName);
+		if (!prop.exists()) {
+			log.warn("Could not find a resource " + resourceName + " in the classpath!");
+		}
+		return prop;
+	}
+
+	/**
+	 * Method return the absolute path to the project root directory. It assumes
+	 * the following structure of the project:
+	 * project-root: 
+	 * conf/settings
+	 * binaries 
+	 * WEB-INF/classes/compbio/engine/conf/PropertyHelperManager.class
+	 * If the structure changes it must be reflected in this method
+	 * 
+	 * @return the local path
+	 * @throws RuntimeException
+	 *             if cannot determine the local path
+	 */
+	public static String getLocalPath() {
+		String clname = ProteoCachePropertyHelperManager.class.getSimpleName();
+		URL url = ProteoCachePropertyHelperManager.class.getResource(clname + ".class");
+		File f = null;
+		try {
+			f = new File(url.toURI());
+			// Iterate up the hierarchy to find a root project directory
+			for (int i = 0; i < 5; i++) {
+				f = f.getParentFile();
+			}
+		} catch (URISyntaxException e) {
+			String mes = "Could not find resources path! Problems locating PropertyHelperManager class! ";
+			log.error(mes + e.getLocalizedMessage(), e.getCause());
+			throw new RuntimeException(mes + e.getLocalizedMessage(), e.getCause());
+		} catch (IllegalArgumentException e) {
+			// Classes are in the jar file, using different method to determine
+			// the path new File(INCORRECT URL) throws it
+			String mes = "It looks like classes are in the jar file. " 
+			           + "Attempting a different method to determinine the path to the resources";
+			log.debug(mes + e.getLocalizedMessage(), e.getCause());
+			try {
+				f = new File(ProteoCachePropertyHelperManager.class.getProtectionDomain().getCodeSource().getLocation().toURI().getPath());
+
+				// Iterate up the hierarchy to find a root project directory
+				// This time there is not need to walk up all class packages
+				// WEB_APPL_NAME\WEB-INF\lib\JAR-FILE-NAME
+				// jws2-1.0\WEB-INF\lib\full-jws2-1.0.jar
+				for (int i = 0; i < 3; i++) {
+					f = f.getParentFile();
+				}
+			} catch (URISyntaxException e1) {
+				log.error("Could not find resources path! " + e1.getLocalizedMessage(), e1.getCause());
+				throw new RuntimeException("Could not find resources path! ", e1.getCause());
+			}
+		}
+		log.debug("Project directory is: " + f.getAbsolutePath());
+		return f.getAbsolutePath() + File.separator;
+	}
+
+	public static int getIntProperty(String propValue) {
+		if (!Util.isEmpty(propValue)) {
+			return Integer.parseInt(propValue.trim());
+		}
+		return -1;
+	}
+
+	public static boolean getBooleanProperty(String propValue) {
+		if (!Util.isEmpty(propValue)) {
+			propValue = propValue.trim();
+			return Boolean.parseBoolean(propValue);
+		}
+		return false;
+	}}
diff --git a/src/main/java/compbio/engine/archive/Archive.java b/src/main/java/compbio/engine/archive/Archive.java
new file mode 100644
index 0000000..2a1f410
--- /dev/null
+++ b/src/main/java/compbio/engine/archive/Archive.java
@@ -0,0 +1,5 @@
+package compbio.engine.archive;
+
+public class Archive {
+
+}
diff --git a/src/main/java/compbio/engine/archive/ArchiveManager.java b/src/main/java/compbio/engine/archive/ArchiveManager.java
new file mode 100644
index 0000000..dabaf3a
--- /dev/null
+++ b/src/main/java/compbio/engine/archive/ArchiveManager.java
@@ -0,0 +1,133 @@
+package compbio.engine.archive;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.InputStream;
+import java.util.Iterator;
+import java.util.Scanner;
+
+//import compbio.util.Util;
+
+/**
+ * Manage files in ProteoCache Archive
+ * 
+ * @author Alexander Sherstnev
+ * @version 1.0 November 2013
+ * 
+ */
+public class ArchiveManager implements Iterator<ArchivedJob> {
+	Archive archive;
+	//private final Scanner input;
+	/**
+	 * Delimiter for the scanner
+	 */
+	//private final String DELIM = ">";
+
+	/**
+	 * Header data can contain non-ASCII symbols and read in UTF8
+	 * 
+	 * @param mainPath
+	 *            the absolute path to the ProteoCache job archive
+	 * @throws FileNotFoundException
+	 *             if the input file is not found
+	 * @throws IllegalStateException
+	 *             if the close method was called on this instance
+	 * 
+	 */
+	public ArchiveManager(final String mainPath) throws FileNotFoundException {
+		/*
+		input = new Scanner(new File(mainPath), "UTF8");
+		input.useDelimiter(DELIM);
+		Runtime.getRuntime().addShutdownHook(new Thread() {
+
+			@Override
+			public void run() {
+				if (input != null) {
+					input.close();
+				}
+			}
+		});
+		*/
+	}
+	
+	public ArchiveManager(Archive ar) {
+		archive = ar;
+	}
+
+
+	/**
+	 * {@inheritDoc}
+	 * 
+	 * @throws IllegalStateException
+	 *             if the close method was called on this instance
+	 */
+	@Override
+	public boolean hasNext() {
+		//return input.hasNext();
+		return true;
+	}
+
+	/**
+	 * Reads the next FastaSequence from the input
+	 * 
+	 * @throws AssertionError
+	 *             if the header or the sequence is missing
+	 * @throws IllegalStateException
+	 *             if the close method was called on this instance
+	 * @throws MismatchException
+	 *             - if there were no more FastaSequence's.
+	 */
+	@Override
+	public ArchivedJob next() {
+		String path = "bla-bla-bla";
+		/*
+		String path = input.next();
+		while (fastaHeader.indexOf("\n") < 0 && input.hasNext()) {
+			path = fastaHeader.concat(">");
+			path = fastaHeader.concat(input.next());
+		}
+		*/
+		return new ArchivedJob(path);
+	}
+
+	/**
+	 * Not implemented
+	 */
+	@Override
+	public void remove() {
+		throw new UnsupportedOperationException();
+	}
+
+	/**
+	 * Call this method to close the connection to the input file if you want to
+	 * free up the resources. The connection will be closed on the JVM shutdown
+	 * if this method was not called explicitly. No further reading on this
+	 * instance of the FastaReader will be possible after calling this method.
+	 */
+	public void close() {
+		//input.close();
+	}
+
+	private static ArchivedJob toFastaSequence(final String singleFastaEntry) {
+
+		// assert !Util.isEmpty(singleFastaEntry) :
+		// "Empty String where FASTA sequence is expected!";
+
+		int nlineidx = singleFastaEntry.indexOf("\n");
+		if (nlineidx < 0) {
+			throw new AssertionError(
+					"The FASTA sequence must contain the header information"
+							+ " separated by the new line from the sequence. Given sequence does not appear to "
+							+ "contain the header! Given data:\n "
+							+ singleFastaEntry);
+		}
+		String header = singleFastaEntry.substring(0, nlineidx);
+
+		/*
+		 * if (Util.isEmpty(sequence)) { throw new AssertionError(
+		 * "Empty sequences are not allowed! Please make sure the " +
+		 * " data is in the FASTA format! Given data:\n " + singleFastaEntry); }
+		 */
+		return new ArchivedJob(header);
+	}
+}
diff --git a/src/main/java/compbio/engine/archive/ArchivedJob.java b/src/main/java/compbio/engine/archive/ArchivedJob.java
new file mode 100644
index 0000000..3f0f7d5
--- /dev/null
+++ b/src/main/java/compbio/engine/archive/ArchivedJob.java
@@ -0,0 +1,44 @@
+package compbio.engine.archive;
+
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.nio.channels.Channels;
+import java.nio.channels.ReadableByteChannel;
+import java.util.List;
+
+public class ArchivedJob {
+	String path;
+	int filesize;
+	List<String> files;
+
+	ArchivedJob (String path) {
+		this.path = path;
+	}
+	
+	public boolean getArchiveFromWS() {
+		return false;
+	}
+	
+	
+	public boolean getArchiveFromWeb (String webpath) throws IOException, MalformedURLException {
+		URL website = new URL(webpath);
+		ReadableByteChannel rbc = Channels.newChannel(website.openStream());
+		FileOutputStream fos = new FileOutputStream(path);
+		fos.getChannel().transferFrom(rbc, 0, Long.MAX_VALUE);
+		return true;
+	}
+	
+	
+	public int getSize() {
+		return filesize;
+	}
+	
+	public List<String> unpack() {
+		if (null != files) {
+			
+		}
+		return files;
+	}
+}
diff --git a/src/main/java/compbio/listeners/ContextListener.java b/src/main/java/compbio/listeners/ContextListener.java
new file mode 100644
index 0000000..ed15609
--- /dev/null
+++ b/src/main/java/compbio/listeners/ContextListener.java
@@ -0,0 +1,178 @@
+package compbio.listeners;
+
+import java.io.IOException;
+import java.util.concurrent.Executors;
+import java.util.concurrent.ScheduledExecutorService;
+import java.util.concurrent.TimeUnit;
+
+import javax.servlet.ServletContextEvent;
+import javax.servlet.ServletContextListener;
+import javax.servlet.annotation.WebListener;
+
+import org.apache.log4j.Logger;
+
+import com.datastax.driver.core.Session;
+
+import compbio.cassandra.CassandraNativeConnector;
+import compbio.cassandra.CassandraNewTableWriter;
+import compbio.cassandra.JpredParserHTTP;
+import compbio.cassandra.JpredParserLocalFile;
+import compbio.engine.ProteoCachePropertyHelperManager;
+import compbio.util.PropertyHelper;
+import compbio.util.Util;
+
+/**
+ * Application Lifecycle Listener implementation class ContextListener
+ * 
+ */
+@WebListener
+public class ContextListener implements ServletContextListener {
+	private ScheduledExecutorService webjob_scheduler;
+	private ScheduledExecutorService localjob_scheduler;
+	private ScheduledExecutorService update_scheduler;
+	CassandraNativeConnector db = new CassandraNativeConnector();
+	static PropertyHelper ph = ProteoCachePropertyHelperManager.getPropertyHelper();
+	private static Logger log = Logger.getLogger(ContextListener.class);
+	public static boolean READ_WEB_JPRED = false;
+	public static boolean READ_LOCALFILE_JPRED = false;
+	public static boolean FILL_NEWTABLE = false;
+
+	private static boolean initBooleanValue(String key) {
+		assert key != null;
+		String status = ph.getProperty(key);
+		log.debug("Loading property: " + key + " with value: " + status);
+		if (Util.isEmpty(status)) {
+			return false;
+		}
+		return new Boolean(status.trim()).booleanValue();
+	}
+
+	/**
+	 * @see ServletContextListener#contextInitialized(ServletContextEvent)
+	 */
+	public void contextInitialized(ServletContextEvent arg0) {
+		System.out.println("ProteoCache session start......");
+		// connect to the db and create table if needed
+		db.Connect();
+		final CassandraNewTableWriter updater = new CassandraNewTableWriter();
+
+		READ_WEB_JPRED = initBooleanValue("cassandra.jpred.web.update");
+		READ_LOCALFILE_JPRED = initBooleanValue("cassandra.jpred.local.update");
+		FILL_NEWTABLE = initBooleanValue("cassandra.newtables.update");
+
+		if (FILL_NEWTABLE) {
+			System.out.println("Initializating new table update scheduler");
+			update_scheduler = Executors.newSingleThreadScheduledExecutor();
+			update_scheduler.schedule(new Runnable() {
+				@Override
+				public void run() {
+					updater.FillNewTable();
+				}
+			}, 10, TimeUnit.SECONDS);
+		}
+
+		if (READ_WEB_JPRED) {
+			// get data from real Jpred production server
+			final String datasrc = "http://www.compbio.dundee.ac.uk/www-jpred/results/usage-new/alljobs.dat";
+			final String prefix = "http://www.compbio.dundee.ac.uk/www-jpred/results";
+			final JpredParserHTTP parser = new JpredParserHTTP(prefix);
+
+			int initialdelay = 300;
+			int updaterate = 600;
+			int newinitialdelay = ProteoCachePropertyHelperManager.getIntProperty(ph.getProperty("cassandra.jpred.web.inidelay"));
+			if (0 <= newinitialdelay) {
+				initialdelay = newinitialdelay;
+			}
+			int newupdaterate = ProteoCachePropertyHelperManager.getIntProperty(ph.getProperty("cassandra.jpred.web.updaterate"));
+			if (0 < newupdaterate) {
+				updaterate = newupdaterate;
+			}
+			final int updateperiod = ProteoCachePropertyHelperManager.getIntProperty(ph.getProperty("cassandra.jpred.web.period"));
+
+			webjob_scheduler = Executors.newSingleThreadScheduledExecutor();
+			System.out.println("Initializating web job scheduler");
+			System.out.println("    initial delay = " + initialdelay + " seconds");
+			System.out.println("    update rate = " + updaterate + " seconds");
+			if (0 < updateperiod)
+				System.out.println("    update period = " + updateperiod + " days");
+			else
+				System.out.println("    update period = 5 days");
+
+			webjob_scheduler.scheduleAtFixedRate(new Runnable() {
+				@Override
+				public void run() {
+					try {
+						if (0 < updateperiod) {
+							parser.Parsing(datasrc, updateperiod);
+						} else {
+							parser.Parsing(datasrc, 5);
+						}
+					} catch (IOException e) {
+						// TODO Auto-generated catch block
+						e.printStackTrace();
+					}
+				}
+			}, initialdelay, updaterate, TimeUnit.SECONDS);
+		}
+
+		if (READ_LOCALFILE_JPRED) {
+			// get irtifical data generated for the DB stress tests
+			final String datasrc = "/home/asherstnev/Projects/Java.projects/proteocache/data_stress_test/data.dat";
+			final String prefix = "/home/asherstnev/Projects/Java.projects/proteocache/data_stress_test/Jpreddata";
+			final JpredParserLocalFile parser = new JpredParserLocalFile(prefix);
+
+			int initialdelay = 300;
+			int updaterate = 600;
+			int newinitialdelay = ProteoCachePropertyHelperManager.getIntProperty(ph.getProperty("cassandra.jpred.local.inidelay"));
+			if (0 <= newinitialdelay) {
+				initialdelay = newinitialdelay;
+			}
+			int newupdaterate = ProteoCachePropertyHelperManager.getIntProperty(ph.getProperty("cassandra.jpred.local.updaterate"));
+			if (0 < newupdaterate) {
+				updaterate = newupdaterate;
+			}
+			final int updateperiod = ProteoCachePropertyHelperManager.getIntProperty(ph.getProperty("cassandra.jpred.local.period"));
+
+			localjob_scheduler = Executors.newSingleThreadScheduledExecutor();
+			System.out.println("Initializating local job scheduler");
+			System.out.println("    initial delay = " + initialdelay + " seconds");
+			System.out.println("    update rate = " + updaterate + " seconds");
+			if (0 < updateperiod)
+				System.out.println("    update period = " + updateperiod + " days");
+			else
+				System.out.println("    update period = 5 days");
+			localjob_scheduler.scheduleAtFixedRate(new Runnable() {
+				@Override
+				public void run() {
+					try {
+						if (0 < updateperiod) {
+							parser.Parsing(datasrc, updateperiod);
+						} else {
+							parser.Parsing(datasrc, 100);
+						}
+					} catch (IOException e) {
+						// TODO Auto-generated catch block
+						e.printStackTrace();
+					}
+				}
+			}, initialdelay, updaterate, TimeUnit.SECONDS);
+		}
+
+	}
+
+	/**
+	 * @see ServletContextListener#contextDestroyed(ServletContextEvent)
+	 */
+	public void contextDestroyed(ServletContextEvent arg0) {
+		db.Closing();
+		System.out.println("Shut down ProteoCache......");
+		if (READ_WEB_JPRED) {
+			webjob_scheduler.shutdownNow();
+		}
+		if (READ_LOCALFILE_JPRED) {
+			localjob_scheduler.shutdownNow();
+		}
+		update_scheduler.shutdownNow();
+	}
+
+}
diff --git a/src/main/java/compbio/listeners/DetailList.java b/src/main/java/compbio/listeners/DetailList.java
new file mode 100644
index 0000000..385ce95
--- /dev/null
+++ b/src/main/java/compbio/listeners/DetailList.java
@@ -0,0 +1,46 @@
+package compbio.listeners;
+
+import java.io.IOException;
+import java.util.List;
+
+import javax.servlet.ServletException;
+import javax.servlet.annotation.WebServlet;
+import javax.servlet.http.HttpServlet;
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
+
+import compbio.cassandra.*;
+import compbio.statistic.StatisticsProt;
+
+/**
+ * Servlet implementation class DetailList
+ */
+@WebServlet("/DetailList")
+public class DetailList extends HttpServlet {
+	private static final long serialVersionUID = 1L;
+
+	/**
+	 * @see HttpServlet#HttpServlet()
+	 */
+
+	/**
+	 * @see HttpServlet#doGet(HttpServletRequest request, HttpServletResponse
+	 *      response)
+	 */
+	protected void doGet(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException {
+		List<DataBase> result;
+		String date1 = request.getParameter("data1");
+		String date2 = request.getParameter("data2");
+		StatisticsProt sp = new StatisticsProt();
+		// result = sp.readDetail(date1, date2);
+	}
+
+	/**
+	 * @see HttpServlet#doPost(HttpServletRequest request, HttpServletResponse
+	 *      response)
+	 */
+	protected void doPost(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException {
+		// TODO Auto-generated method stub
+	}
+
+}
diff --git a/src/main/java/compbio/listeners/ServletJobsByDate.java b/src/main/java/compbio/listeners/ServletJobsByDate.java
new file mode 100644
index 0000000..4aee8be
--- /dev/null
+++ b/src/main/java/compbio/listeners/ServletJobsByDate.java
@@ -0,0 +1,52 @@
+package compbio.listeners;
+
+import java.io.IOException;
+import java.util.Calendar;
+import java.util.List;
+
+import javax.servlet.RequestDispatcher;
+import javax.servlet.ServletException;
+import javax.servlet.annotation.WebServlet;
+import javax.servlet.http.HttpServlet;
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
+
+import compbio.cassandra.DataBase;
+import compbio.statistic.CassandraRequester;
+import compbio.statistic.StatisticsProt;
+
+@WebServlet("/ServletJobsByDate")
+public class ServletJobsByDate extends HttpServlet {
+	private static final long serialVersionUID = 1L;
+
+	/**
+	 * @see HttpServlet#doPost(HttpServletRequest request, HttpServletResponse
+	 *      response)
+	 */
+	protected void doGet(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException {
+		final long startTime = System.currentTimeMillis();
+		String date1 = request.getParameter("data1");
+		String date2 = request.getParameter("data2");
+		CassandraRequester cr = new CassandraRequester();
+		if (null != request.getParameter("option")) {
+			Calendar cal = Calendar.getInstance();
+			date1 = StatisticsProt.DateFormatYYMMDD(cr.earliestDate());
+			date2 = cal.get(Calendar.YEAR) + "/" + (cal.get(Calendar.MONTH) + 1) + "/" + cal.get(Calendar.DAY_OF_MONTH);
+		}
+		request.setAttribute("data1", date1);
+		request.setAttribute("data2", date2);
+		List<DataBase> res = cr.countJobs(date1, date2);
+		request.setAttribute("result", res);
+		final long endTime = System.currentTimeMillis();
+		request.setAttribute("timeExecution", (endTime - startTime));
+		System.out.println ("QueryServlet.doGet: total number of dates = " + res.size());
+		request.setAttribute("flag", request.getParameter("option"));
+		RequestDispatcher rd = request.getRequestDispatcher("/ReportJobsByDate.jsp");
+		rd.forward(request, response);
+	}
+
+	protected void doPost(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException {
+		doGet(request, response);
+	}
+
+}
diff --git a/src/main/java/compbio/listeners/ServletLogInfo.java b/src/main/java/compbio/listeners/ServletLogInfo.java
new file mode 100644
index 0000000..87c8f92
--- /dev/null
+++ b/src/main/java/compbio/listeners/ServletLogInfo.java
@@ -0,0 +1,46 @@
+package compbio.listeners;
+
+import java.io.IOException;
+
+import javax.servlet.RequestDispatcher;
+import javax.servlet.ServletException;
+import javax.servlet.annotation.WebServlet;
+import javax.servlet.http.HttpServlet;
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
+
+import compbio.statistic.CassandraRequester;
+
+
+/**
+ * Servlet implementation class LogServlet
+ */
+@WebServlet("/ServletLogInfo")
+public class ServletLogInfo extends HttpServlet {
+	private static final long serialVersionUID = 1L;
+       
+    
+
+	/**
+	 * @see HttpServlet#doGet(HttpServletRequest request, HttpServletResponse response)
+	 */
+	protected void doGet(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException {
+		final long startTime = System.currentTimeMillis();
+		String id = request.getParameter("IdJob");
+		CassandraRequester cr = new CassandraRequester();
+		request.setAttribute("result", cr.readJobLog(id));
+		final long endTime = System.currentTimeMillis();
+		request.setAttribute("timeExecution", (endTime - startTime));
+		request.setAttribute("IdJob", id);
+		RequestDispatcher rd = request.getRequestDispatcher("/ReportLogInfo.jsp");
+		rd.forward(request, response);
+	}
+
+	/**
+	 * @see HttpServlet#doPost(HttpServletRequest request, HttpServletResponse response)
+	 */
+	protected void doPost(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException {
+		doGet(request, response);
+	}
+
+}
diff --git a/src/main/java/compbio/listeners/ServletSequenceProtein.java b/src/main/java/compbio/listeners/ServletSequenceProtein.java
new file mode 100644
index 0000000..94df90c
--- /dev/null
+++ b/src/main/java/compbio/listeners/ServletSequenceProtein.java
@@ -0,0 +1,56 @@
+package compbio.listeners;
+
+import java.io.IOException;
+
+import javax.servlet.RequestDispatcher;
+import javax.servlet.ServletException;
+import javax.servlet.annotation.WebServlet;
+import javax.servlet.http.HttpServlet;
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
+
+import compbio.statistic.CassandraRequester;
+import compbio.statistic.StatisticsProt;
+
+/**
+ * Servlet implementation class ProtServlet
+ */
+@WebServlet("/ServletSequenceProtein")
+public class ServletSequenceProtein extends HttpServlet {
+	private static final long serialVersionUID = 1L;
+
+	/**
+	 * @see HttpServlet#doGet(HttpServletRequest request, HttpServletResponse
+	 *      response)
+	 */
+	protected void doGet(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException {
+		final long startTime = System.currentTimeMillis();
+		String flag = request.getParameter("protein");
+		String prot = request.getParameter("prot");
+		String search = request.getParameter("Search");
+		int counter = Integer.parseInt(request.getParameter("counterJob"));
+		CassandraRequester cr = new CassandraRequester();
+		if (search.equals("Search counter")) {
+	 		request.setAttribute("result", cr.readProteinByCounter(counter));
+		} else {
+				request.setAttribute("result", cr.readProteins(prot, flag));
+		}
+		final long endTime = System.currentTimeMillis();
+		request.setAttribute("timeExecution", (endTime - startTime));
+		request.setAttribute("prot", prot);
+		request.setAttribute("flag", flag);
+		request.setAttribute("search", search);
+		request.setAttribute("counter", counter);
+		RequestDispatcher rd = request.getRequestDispatcher("/ReportSequenceProtein.jsp");
+		rd.forward(request, response);
+	}
+
+	/**
+	 * @see HttpServlet#doPost(HttpServletRequest request, HttpServletResponse
+	 *      response)
+	 */
+	protected void doPost(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException {
+		doGet(request, response);
+	}
+
+}
diff --git a/src/main/java/compbio/listeners/ServletTimeExecution.java b/src/main/java/compbio/listeners/ServletTimeExecution.java
new file mode 100644
index 0000000..c380604
--- /dev/null
+++ b/src/main/java/compbio/listeners/ServletTimeExecution.java
@@ -0,0 +1,54 @@
+package compbio.listeners;
+
+import java.io.IOException;
+import java.util.Calendar;
+
+import javax.servlet.RequestDispatcher;
+import javax.servlet.ServletException;
+import javax.servlet.annotation.WebServlet;
+import javax.servlet.http.HttpServlet;
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
+
+import compbio.statistic.StatisticsProt;
+import compbio.statistic.CassandraRequester;
+
+/**
+ * Servlet implementation class LengthServlet
+ */
+@WebServlet("/ServletTimeExecution")
+public class ServletTimeExecution extends HttpServlet {
+	private static final long serialVersionUID = 1L;
+
+	/**
+	 * @see HttpServlet#doGet(HttpServletRequest request, HttpServletResponse
+	 *      response)
+	 */
+	protected void doGet(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException {
+		final long startTime = System.currentTimeMillis();
+		String date1 = request.getParameter("data1");
+		String date2 = request.getParameter("data2");
+		CassandraRequester sp = new CassandraRequester();
+		if (null != request.getParameter("option")) {
+			Calendar cal = Calendar.getInstance();
+			date1 = StatisticsProt.DateFormatYYMMDD(sp.earliestDate());
+			date2 = cal.get(Calendar.YEAR) + "/" + (cal.get(Calendar.MONTH) + 1) + "/" + cal.get(Calendar.DAY_OF_MONTH);
+		}
+		request.setAttribute("data1", date1);
+		request.setAttribute("data2", date2);
+		request.setAttribute("result", sp.extractExecutionTime(date1, date2));
+		request.setAttribute("flag", request.getParameter("option"));
+		final long endTime = System.currentTimeMillis();
+		request.setAttribute("timeExecution", (endTime - startTime));
+		RequestDispatcher rd = request.getRequestDispatcher("/ReportTimeExecution.jsp");
+		rd.forward(request, response);
+	}
+
+	/**
+	 * @see HttpServlet#doPost(HttpServletRequest request, HttpServletResponse
+	 *      response)
+	 */
+	protected void doPost(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException {
+		doGet(request, response);
+	}
+}
diff --git a/src/main/java/compbio/statistic/CassandraRequester.java b/src/main/java/compbio/statistic/CassandraRequester.java
new file mode 100755
index 0000000..2da38e7
--- /dev/null
+++ b/src/main/java/compbio/statistic/CassandraRequester.java
@@ -0,0 +1,287 @@
+package compbio.statistic;
+
+import java.text.ParseException;
+import java.text.SimpleDateFormat;
+import java.util.ArrayList;
+import java.util.Calendar;
+import java.util.Date;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+
+import compbio.cassandra.CassandraNativeConnector;
+import compbio.cassandra.CassandraReader;
+import compbio.cassandra.DataBase;
+import compbio.cassandra.Pair;
+import compbio.cassandra.StructureJobLog;
+import compbio.cassandra.StructureProteinPrediction;
+
+public class CassandraRequester {
+	private CassandraReader db = new CassandraReader();
+	private ArrayList<DataBase> query;
+	private static long currentDate = 0;
+	private static long earlestDate = 0;
+
+	/*
+	 * query: execution time for the period from date1 till date2
+	 */
+	public List<DataBase> extractExecutionTime(String date1, String date2) {
+		if (null == date1) {
+			date1 = "1970/1/1";
+		}
+		if (null == date2) {
+			date1 = "2100/1/1";
+		}
+		if (!isThisDateValid(date1) || !isThisDateValid(date2)) {
+			System.out.println("Wrong date: point 3");
+			return null;
+		}
+		SetDateRange();
+		int nbins = 5;
+		long dateStart = DateParsing(date1);
+		long dateEnd = DateParsing(date2);
+		if (dateEnd < earlestDate || dateStart > currentDate || dateStart > dateEnd)
+			return null;
+		if (dateStart < earlestDate)
+			dateStart = earlestDate;
+		if (dateEnd > currentDate)
+			dateStart = currentDate;
+
+		Calendar start = Calendar.getInstance();
+		start.setTime(new Date(dateStart));
+		Calendar end = Calendar.getInstance();
+		end.setTime(new Date(dateEnd));
+		query = new ArrayList<DataBase>();
+		List<Integer> totalTime = new ArrayList<Integer>();
+		for (int i = 0; i < nbins; i++)
+			totalTime.add(i, 0);
+		List<Pair<String, String>> res = db.ReadProteinDataTable();
+		List<Pair<Date, Long>> numres = new ArrayList<Pair<Date, Long>>();
+
+		for (Pair<String, String> entry : res) {
+			SimpleDateFormat dateformatter = new SimpleDateFormat("yyyy/MM/dd");
+			try {
+				Date jobstartdate = dateformatter.parse(entry.getElement0());
+				long date = jobstartdate.getTime();
+				if (dateStart <= date && date <= dateEnd) {
+					SimpleDateFormat datetimeformatter = new SimpleDateFormat("yyyy/MM/dd:H:m:s");
+					Date jobstarttime = datetimeformatter.parse(entry.getElement0());
+					Date jobendtime = datetimeformatter.parse(entry.getElement1());
+					long diff = (jobendtime.getTime() - jobstarttime.getTime()) / 1000;
+					Pair<Date, Long> pair = new Pair<Date, Long>(jobstartdate, Long.valueOf(diff));
+					numres.add(pair);
+				}
+			} catch (ParseException e) {
+				e.printStackTrace();
+			}
+		}
+
+		for (Date date = start.getTime(); !start.after(end); start.add(Calendar.DATE, 1), date = start.getTime()) {
+			List<Integer> timeResult = new ArrayList<Integer>();
+			for (int i = 0; i < nbins; i++)
+				timeResult.add(i, 0);
+			for (Pair<Date, Long> p : numres) {
+				if (date.equals(p.getElement0())) {
+					long lenResult = p.getElement1().longValue();
+					if (lenResult <= 30)
+						timeResult.set(0, timeResult.get(0) + 1);
+					else if (lenResult > 30 && lenResult <= 60)
+						timeResult.set(1, timeResult.get(1) + 1);
+					else if (lenResult > 60 && lenResult <= 120)
+						timeResult.set(2, timeResult.get(2) + 1);
+					else if (lenResult > 120 && lenResult <= 600)
+						timeResult.set(3, timeResult.get(3) + 1);
+					else {
+						timeResult.set(4, timeResult.get(4) + 1);
+					}
+				}
+			}
+			for (int i = 0; i < nbins; i++)
+				totalTime.set(i, totalTime.get(i) + timeResult.get(i));
+			DataBase db = new DataBase();
+			db.setTimeRez(timeResult);
+			db.setDate(DateFormat(date.getTime()));
+			query.add(db);
+		}
+
+		DataBase db = new DataBase();
+		db.setTimeTotalExec(totalTime);
+		query.add(db);
+		System.out.println("StatisticsProt.readLength: total number of dates = " + query.size());
+		return query;
+	}
+	
+	/*
+	 * query: total number of jobs  for the period from date1 till date2
+	 */
+	public List<DataBase> countJobs(String date1, String date2) {
+		if (null == date1) {
+			date1 = "1970/1/1";
+		}
+		if (null == date2) {
+			date1 = "2100/1/1";
+		}
+		if (!isThisDateValid(date1) || !isThisDateValid(date2)) {
+			System.out.println("Wrong date: point 3");
+			return null;
+		}
+		SetDateRange();
+		long dateStart = DateParsing(date1);
+		long dateEnd = DateParsing(date2);
+		if (dateEnd < earlestDate || dateStart > currentDate || dateStart > dateEnd)
+			return null;
+		if (dateStart < earlestDate)
+			dateStart = earlestDate;
+		if (dateEnd > currentDate)
+			dateStart = currentDate;
+
+		Calendar start = Calendar.getInstance();
+		start.setTime(new Date(dateStart));
+		Calendar end = Calendar.getInstance();
+		end.setTime(new Date(dateEnd));
+		query = new ArrayList<DataBase>();
+		for (Date date = start.getTime(); !start.after(end); start.add(Calendar.DATE, 1), date = start.getTime()) {
+			long res = db.ReadDateTable(date.getTime());
+			DataBase db = new DataBase();
+			db.setTotal((int)res);
+			db.setDate(DateFormat(date.getTime()));
+			query.add(db);
+		}
+		System.out.println("StatisticsProt.readLength: total number of dates = " + query.size());
+		return query;
+	}
+	/* 
+	 * query: protein sequence
+	 * */
+	public List<DataBase> readProteins(String protIn, String flag) {
+		query = new ArrayList<DataBase>();
+		List<StructureProteinPrediction> res;
+		if (flag.equals("whole")) 
+			res = db.ReadWholeSequence(protIn);
+		 else 
+			res = db.ReadPartOfSequence(protIn);
+		for (StructureProteinPrediction entry : res) {
+			Map<String,String> pred = entry.getPrediction();
+			Iterator it = pred.entrySet().iterator();
+			while (it.hasNext()) {
+				DataBase db = new DataBase();
+				db.setProt(entry.getSequence());
+				Map.Entry pairs = (Map.Entry)it.next();
+				db.setId(entry.getJobid());
+				db.setJpred(pairs.getValue().toString());
+				if (flag.equals("part"))
+					db.setSubProt(CreateSubprot (entry.getSequence(), protIn));				
+				query.add(db);
+			}
+		}
+		return query;
+	}
+	
+	/* 
+	 * query protein sequences with number of jobs
+	 */
+	public List<DataBase> readProteinByCounter(int minimalcounter) {
+		query = new ArrayList<DataBase>();
+		Map<String, Integer> map = db.ReadProteinSequenceByCounter();
+		for (Map.Entry<String, Integer> entry : map.entrySet()) {
+			if (entry.getValue() > minimalcounter) {
+				DataBase db = new DataBase();
+				db.setTotalId(entry.getValue());
+				db.setProt(entry.getKey());
+				query.add(db);
+			}
+		}
+		return query;
+	}
+	
+	/*
+	 * query jobs log info
+	 */
+	public DataBase readJobLog(String jobid) {
+	//	query = new ArrayList<DataBase>();
+		StructureJobLog res = db.ReadJobLog(jobid);
+		DataBase query = new DataBase();
+		query.setLogInfo(res);
+	//	query.setres);
+		return query;
+	}
+	/*
+	 * create list of parts of protein sequence;
+	 */
+	private static List<String> CreateSubprot (String protein, String subprot) {
+		List<String> sub = new ArrayList<String>();
+		String subStr = protein;
+		while (subStr.length() > 0 && subStr.contains(subprot)) {
+			String first = subStr.substring(0, subStr.indexOf(subprot));
+			if (first.length() > 0)
+				sub.add(first);
+			sub.add(subprot);
+			subStr = subStr.substring(subStr.indexOf(subprot) + subprot.length(), subStr.length());
+		}
+		if (subStr.length() > 0)
+			sub.add(subStr);
+		return sub;
+	}
+	/*
+	 * convert String date into long date (miliseconds since the epoch start)
+	 */
+	private static long DateParsing(String datInput) {
+		if (datInput == null) {
+			return 0;
+		}
+		long dateWorkSt = 0;
+		SimpleDateFormat formatter = new SimpleDateFormat("yyyy/MM/dd");
+		try {
+			dateWorkSt = formatter.parse(datInput).getTime();
+		} catch (ParseException e) {
+			e.printStackTrace();
+		}
+		return dateWorkSt;
+	}
+
+	// convert long to date in string format
+	private static String DateFormat(long inDate) {
+		SimpleDateFormat datformat = new SimpleDateFormat("dd/MM/yyyy");
+		return datformat.format(new Date(inDate));
+	}
+
+	/*
+	 * set earlest date and current dates. earlestDate is static and should be
+	 * set at the 1st call currentDate should be re-calculated every time
+	 */
+	private static void SetDateRange() {
+		Calendar cal = Calendar.getInstance();
+		currentDate = DateParsing(cal.get(Calendar.YEAR) + "/" + (cal.get(Calendar.MONTH) + 1) + "/" + cal.get(Calendar.DAY_OF_MONTH));
+		if (0 == earlestDate) {
+			CassandraRequester cr = new CassandraRequester();
+			earlestDate = cr.earliestDate();
+			System.out.println("Set earlest Date = " + earlestDate);
+		}
+	}
+
+	public boolean isThisDateValid(String dateToValidate) {
+		if (dateToValidate == null || dateToValidate.equals("")) {
+			System.out.println("Undefined date");
+			return false;
+		}
+		SimpleDateFormat sdf = new SimpleDateFormat("yyyy/MM/dd");
+		try {
+			// if not valid, this will throw ParseException
+			sdf.setLenient(false);
+			Date date = sdf.parse(dateToValidate);
+		} catch (ParseException e) {
+			e.printStackTrace();
+			return false;
+		}
+		return true;
+	}
+
+	/*
+	 * find the earliest date in the database
+	 */
+	public long earliestDate() {
+		earlestDate = CassandraNativeConnector.getEarliestDateInDB();
+		return earlestDate;
+	}
+	
+}
diff --git a/src/main/java/compbio/statistic/StatisticsProt.java b/src/main/java/compbio/statistic/StatisticsProt.java
new file mode 100755
index 0000000..05375c0
--- /dev/null
+++ b/src/main/java/compbio/statistic/StatisticsProt.java
@@ -0,0 +1,402 @@
+package compbio.statistic;
+
+import java.text.ParseException;
+import java.text.SimpleDateFormat;
+import java.util.ArrayList;
+import java.util.Calendar;
+import java.util.Collections;
+import java.util.Date;
+import java.util.Iterator;
+import java.util.List;
+
+import compbio.cassandra.CassandraNativeConnector;
+import compbio.cassandra.DataBase;
+
+public class StatisticsProt {
+	private CassandraNativeConnector cc = new CassandraNativeConnector();
+	private ArrayList<DataBase> query;
+	private static long currentDate = 0;
+	private static long earlestDate = 0;
+
+	/* 
+	 * query: the period from date1 till date2
+	 * */
+	public List<DataBase> readDetails(String date1, String date2) {
+
+		if (!isThisDateValid(date1) || !isThisDateValid(date2)) {
+			System.out.println("Wrong date: point 1");
+			return null;
+		}
+		SetDateRange();
+		long dateStart = DateParsing(date1);
+		long dateEnd = DateParsing(date2);
+		if ((dateStart < earlestDate && dateEnd < earlestDate) || (dateStart > currentDate && dateEnd > currentDate) || dateStart > dateEnd)
+			return null;
+		if (dateStart < earlestDate)
+			dateStart = earlestDate;
+		if (dateEnd > currentDate)
+			dateStart = currentDate;
+		System.out.println("StatisticsProt.readDetails: earlestDate = " + earlestDate + ", currentDate = " + currentDate);
+		System.out.println("StatisticsProt.readDetails: Start date " + date1 + ": int representation = " + dateStart);
+		System.out.println("StatisticsProt.readDetails: End date " + date2 + ": int representation = " + dateEnd);
+		Calendar start = Calendar.getInstance();
+		start.setTime(new Date(dateStart));
+		Calendar end = Calendar.getInstance();
+		end.setTime(new Date(dateEnd));
+		query = new ArrayList<DataBase>();
+		int day = 0;
+		/*
+		for (Date date = start.getTime(); !start.after(end); start.add(Calendar.DATE, 1), date = start.getTime()) {
+			SliceQuery<Long, String, String> result = HFactory.createSliceQuery(cc.GetKeyspace(), LongSerializer.get(),
+					StringSerializer.get(), StringSerializer.get());
+			result.setColumnFamily("ProteinData");
+			result.setKey(date.getTime());
+			result.setRange(null, null, false, Integer.MAX_VALUE);
+			QueryResult<ColumnSlice<String, String>> columnSlice = result.execute();
+			++day;
+			System.out.print("Day " + day + ": dataStart = " + date + ": ");
+			if (!columnSlice.get().getColumns().isEmpty()) {
+				DataBase db = new DataBase(DateFormat(date.getTime()), columnSlice.get().getColumns().size());
+				query.add(db);
+				System.out.println("data exist");
+			} else {
+				System.out.println("no data");
+			}
+		}
+		*/
+		System.out.println("StatisticsProt.readLength: total number of dates = " + query.size());
+		return query;
+	}
+
+	/*
+	 * query: execution time for the period from date1 till date2
+	 * */
+	public List<DataBase> readLength(String date1, String date2) {
+		if (!isThisDateValid(date1) || !isThisDateValid(date2)) {
+			System.out.println("Wrong date: point 3");
+			return null;
+		}
+		SetDateRange();
+		int nbins = 5;
+		long dateStart = DateParsing(date1);
+		long dateEnd = DateParsing(date2);
+		if ((dateStart < earlestDate && dateEnd < earlestDate) || (dateStart > currentDate && dateEnd > currentDate) || dateStart > dateEnd)
+			return null;
+		if (dateStart < earlestDate)
+			dateStart = earlestDate;
+		if (dateEnd > currentDate)
+			dateStart = currentDate;
+		System.out.println("StatisticsProt.readLength: earlestDate = " + earlestDate + ", currentDate = " + currentDate);
+		System.out.println("StatisticsProt.readLength: Start date is " + date1 + ": int representation = " + dateStart);
+		System.out.println("StatisticsProt.readLength: End date is " + date2 + ": int representation = " + dateEnd);
+		Calendar start = Calendar.getInstance();
+		start.setTime(new Date(dateStart));
+		Calendar end = Calendar.getInstance();
+		end.setTime(new Date(dateEnd));
+		query = new ArrayList<DataBase>();
+		List<Integer> totalTime = new ArrayList<Integer>();
+		for (int i = 0; i < nbins; i++)
+			totalTime.add(i, 0);
+		/*
+		for (Date date = start.getTime(); !start.after(end); start.add(Calendar.DATE, 1), date = start.getTime()) {
+			List<Integer> timeResult = new ArrayList<Integer>();
+			SliceQuery<Long, String, String> result = HFactory.createSliceQuery(cc.GetKeyspace(), LongSerializer.get(),
+					StringSerializer.get(), StringSerializer.get());
+			result.setColumnFamily("ProteinData");
+			result.setKey(date.getTime());
+			result.setRange(null, null, false, Integer.MAX_VALUE);
+			QueryResult<ColumnSlice<String, String>> columnSlice = result.execute();
+			List<HColumn<String, String>> col = columnSlice.get().getColumns();
+			if (!col.isEmpty()) {
+				Iterator<HColumn<String, String>> itCol = col.iterator();
+				for (int i = 0; i < nbins; i++)
+					timeResult.add(i, 0);
+				// split all jobs into nbins bins
+				while (itCol.hasNext()) {
+					String id = itCol.next().getName();
+					long lenResult = CountID(id);
+					if (lenResult <= 30)
+						timeResult.set(0, timeResult.get(0) + 1);
+					else if (lenResult > 30 && lenResult <= 60)
+						timeResult.set(1, timeResult.get(1) + 1);
+					else if (lenResult > 60 && lenResult <= 120)
+						timeResult.set(2, timeResult.get(2) + 1);
+					else if (lenResult > 120 && lenResult <= 600)
+						timeResult.set(3, timeResult.get(3) + 1);
+					else {
+						timeResult.set(4, timeResult.get(4) + 1);
+					}
+				}
+				for (int i = 0; i < nbins; i++)
+					totalTime.set(i, totalTime.get(i) + timeResult.get(i));
+				DataBase db = new DataBase();
+				db.setTimeRez(timeResult);
+				db.setDate(DateFormat(date.getTime()));
+				query.add(db);
+			}
+		}
+		*/
+		DataBase db = new DataBase();
+		db.setTimeTotalExec(totalTime);
+		query.add(db);
+		System.out.println("StatisticsProt.readLength: total number of dates = " + query.size());
+		return query;
+	}
+
+	/* 
+	 * query: protein sequence
+	 * */
+	public List<DataBase> readProteins(String protIn) {
+		query = new ArrayList<DataBase>();
+		/*
+		SliceQuery<String, String, String> result = HFactory.createSliceQuery(cc.GetKeyspace(), StringSerializer.get(),
+				StringSerializer.get(), StringSerializer.get());
+		result.setColumnFamily("ProteinRow");
+		result.setKey(protIn);
+		result.setRange(null, null, false, Integer.MAX_VALUE);
+		QueryResult<ColumnSlice<String, String>> columnSlice = result.execute();
+		Iterator<HColumn<String, String>> it = columnSlice.get().getColumns().iterator();
+		while (it.hasNext()) {
+			HColumn<String, String> col = it.next();
+			String name = col.getName();
+			if (name.matches("(.*)jnetpred")) {
+				DataBase db = new DataBase();
+				db.setProt(protIn);
+				db.setId(col.getName());
+				db.setJpred(col.getValue());
+				query.add(db);
+			}
+		}
+		*/
+		return query;
+	}
+
+	/* 
+	 * query by a protein sequence
+	 * */
+	public List<DataBase> readProtID(int counter) {
+		query = new ArrayList<DataBase>();
+		int row_count = 100;
+		/*
+		RangeSlicesQuery<String, String, String> result = HFactory.createRangeSlicesQuery(cc.GetKeyspace(), StringSerializer.get(),
+				StringSerializer.get(), StringSerializer.get());
+		result.setColumnFamily("ProteinRow");
+		result.setRange(null, null, false, 100);
+		result.setRowCount(row_count);
+		String last_key = null;
+		while (true) {
+			result.setKeys(last_key, null);
+			QueryResult<OrderedRows<String, String, String>> columnSlice = result.execute();
+			OrderedRows<String, String, String> rows = columnSlice.get();
+			Iterator<Row<String, String, String>> rowsIterator = rows.iterator();
+			while (rowsIterator.hasNext()) {
+				Row<String, String, String> row = rowsIterator.next();
+				last_key = row.getKey();
+				List<HColumn<String, String>> clms = row.getColumnSlice().getColumns();
+				//int npred = 0;
+				//for (HColumn<String, String> cln : clms) {
+				//	String name = cln.getName();
+				//	if (name.matches("(.*)jnetpred")) {
+				//		++npred;
+				//	}
+				//}
+				int npred = clms.size();
+				if (npred > counter) {
+					DataBase db = new DataBase();
+					db.setProt(last_key);
+					db.setTotalId(npred);
+					query.add(db);
+				}
+			}
+			if (rows.getCount() < row_count)
+				break;
+		}*/
+		return query;
+	}
+
+	/* 
+	 * query by a part of sequence
+	 * */
+	public List<DataBase> readPart(String protIn) {
+		int row_count = 10000;
+		query = new ArrayList<DataBase>();
+		/*
+		RangeSlicesQuery<String, String, String> result = HFactory.createRangeSlicesQuery(cc.GetKeyspace(), StringSerializer.get(),
+				StringSerializer.get(), StringSerializer.get());
+		result.setColumnFamily("ProteinRow");
+		result.setRange(null, null, false, Integer.MAX_VALUE);
+		result.setRowCount(row_count);
+		String last_key = null;
+		while (true) {
+			result.setKeys(last_key, null);
+			QueryResult<OrderedRows<String, String, String>> columnSlice = result.execute();
+			OrderedRows<String, String, String> rows = columnSlice.get();
+			Iterator<Row<String, String, String>> rowsIterator = rows.iterator();
+			while (rowsIterator.hasNext()) {
+				Row<String, String, String> row = rowsIterator.next();
+				last_key = row.getKey();
+				if (last_key.matches("(.*)" + protIn + "(.*)")) {
+					Iterator<HColumn<String, String>> it = row.getColumnSlice().getColumns().iterator();
+					while (it.hasNext()) {
+						HColumn<String, String> col = it.next();
+						List<String> subProt = new ArrayList<String>();
+						String subStr = last_key;
+						while (subStr.length() > 0 && subStr.contains(protIn)) {
+							String first = subStr.substring(0, subStr.indexOf(protIn));
+							if (first.length() > 0)
+								subProt.add(first);
+							subProt.add(protIn);
+							subStr = subStr.substring(subStr.indexOf(protIn) + protIn.length(), subStr.length());
+						}
+						if (subStr.length() > 0)
+							subProt.add(subStr);
+						String name = col.getName();
+						if (name.matches("(.*)jnetpred")) {
+							DataBase db = new DataBase();
+							db.setProt(last_key);
+							db.setId(col.getName());
+							db.setJpred(col.getValue());
+							db.setSubProt(subProt);
+							query.add(db);
+						}
+					}
+				}
+			}
+			if (rows.getCount() < row_count)
+				break;
+		}
+		*/
+		return query;
+	}
+
+	/* 
+	 * convert String date into long date (miliseconds since the epoch start)
+	 */
+	private static long DateParsing(String datInput) {
+		if (datInput == null) {
+			return 0;
+		}
+		long dateWorkSt = 0;
+		SimpleDateFormat formatter = new SimpleDateFormat("yyyy/MM/dd");
+		try {
+			dateWorkSt = formatter.parse(datInput).getTime();
+		} catch (ParseException e) {
+			e.printStackTrace();
+		}
+		return dateWorkSt;
+	}
+
+	/*
+	 * convert String date:time into long date:time (miliseconds since the epoch start)
+	 */
+	private static long TimeConvert(String datInput) {
+		long dateWorkSt = 0;
+		if (datInput == null) {
+			return dateWorkSt;
+		}
+		SimpleDateFormat formatter = new SimpleDateFormat("yyyy/MM/dd:hh:mm:ss");
+		try {
+			dateWorkSt = formatter.parse(datInput).getTime();
+		} catch (ParseException e) {
+			e.printStackTrace();
+		}
+		return dateWorkSt;
+	}
+
+	// convert long to date in string format
+	private static String DateFormat(long inDate) {
+		SimpleDateFormat datformat = new SimpleDateFormat("dd/MM/yyyy");
+		String dateString = datformat.format(new Date(inDate));
+		return dateString;
+	}
+
+	/*
+	 * convert ???
+	 */
+	public static String DateFormatYYMMDD(long indate) {
+		SimpleDateFormat datformat = new SimpleDateFormat("yyyy/MM/dd");
+		String dateString = datformat.format(new Date(indate));
+		return dateString;
+	}
+
+	/*
+	 * ???
+	 */
+	public long CountID(String id) {
+		/*
+		SliceQuery<String, String, String> sliceQuery = HFactory.createSliceQuery(cc.GetKeyspace(), StringSerializer.get(),
+				StringSerializer.get(), StringSerializer.get());
+		sliceQuery.setColumnFamily("ProteinLog").setKey(id).setRange("", "", false, 100);
+		QueryResult<ColumnSlice<String, String>> result = sliceQuery.execute();
+		String datBegin = result.get().getColumnByName("DataBegin").getValue();
+		String datEnd = result.get().getColumnByName("DataEnd").getValue();
+
+		long datBeginLong = TimeConvert(datBegin);
+		long datEndLong = TimeConvert(datEnd);
+		return (datEndLong - datBeginLong) / 1000;
+		*/
+		return 0;
+	}
+
+	/*
+	 * set earlest date and current dates. 
+	 * earlestDate is static and should be set at the 1st call
+	 * currentDate should be re-calculated every time
+	 */
+	private static void SetDateRange() {
+		if (0 == earlestDate) {
+			StatisticsProt sp = new StatisticsProt();
+			earlestDate = sp.earliestDate();
+			System.out.println("Set earlest Date = " + earlestDate);
+		}
+		Calendar cal = Calendar.getInstance();
+		currentDate = DateParsing(cal.get(Calendar.YEAR) + "/" + (cal.get(Calendar.MONTH) + 1) + "/" + cal.get(Calendar.DAY_OF_MONTH));
+	}
+
+	public boolean isThisDateValid(String dateToValidate) {
+		if (dateToValidate == null || dateToValidate.equals("")) {
+			System.out.println("Undefined date");
+			return false;
+		}
+		SimpleDateFormat sdf = new SimpleDateFormat("yyyy/MM/dd");
+		try {
+			// if not valid, this will throw ParseException
+			sdf.setLenient(false);
+			Date date = sdf.parse(dateToValidate);
+		} catch (ParseException e) {
+			e.printStackTrace();
+			return false;
+		}
+		return true;
+	}
+
+	/*
+	 * find the earliest date in the database
+	 */
+	public long earliestDate() {
+		ArrayList<Long> dateSort = new ArrayList<Long>();
+		int row_count = 10000;
+		/*
+		RangeSlicesQuery<Long, String, String> result = HFactory.createRangeSlicesQuery(cc.GetKeyspace(), LongSerializer.get(),
+				StringSerializer.get(), StringSerializer.get());
+		result.setColumnFamily("ProteinData");
+		result.setRange(null, null, false, Integer.MAX_VALUE);
+		result.setRowCount(row_count);
+		Long last_key = null;
+		while (true) {
+			result.setKeys(last_key, null);
+			QueryResult<OrderedRows<Long, String, String>> columnSlice = result.execute();
+			OrderedRows<Long, String, String> rows = columnSlice.get();
+			Iterator<Row<Long, String, String>> rowsIterator = rows.iterator();
+			while (rowsIterator.hasNext()) {
+				Row<Long, String, String> row = rowsIterator.next();
+				last_key = row.getKey();
+				dateSort.add(last_key);
+			}
+			if (rows.getCount() < row_count)
+				break;
+		}*/
+		Collections.sort(dateSort);
+		return dateSort.get(0);
+	}
+}
diff --git a/src/main/resources/META-INF/MANIFEST.MF b/src/main/resources/META-INF/MANIFEST.MF
new file mode 100644
index 0000000..5e94951
--- /dev/null
+++ b/src/main/resources/META-INF/MANIFEST.MF
@@ -0,0 +1,3 @@
+Manifest-Version: 1.0
+Class-Path: 
+
diff --git a/src/main/resources/doc/packages.odt b/src/main/resources/doc/packages.odt
new file mode 100644
index 0000000..246b4bf
Binary files /dev/null and b/src/main/resources/doc/packages.odt differ
diff --git a/src/main/resources/log4j.properties b/src/main/resources/log4j.properties
new file mode 100644
index 0000000..d186883
--- /dev/null
+++ b/src/main/resources/log4j.properties
@@ -0,0 +1,66 @@
+## Uncomment to enable ProteoCache activity logging
+## Valid log levels are:
+## TRACE - log everything from below including very detailed messages (useful for debugging only)
+## DEBUG - log everything from below including some minor events (useful for debugging only)
+## INFO - log everything from below including some information messages
+## WARN - log error and warnings
+## ERROR - log errors and fatal events only 
+## FATAL - log fatal events only
+
+# To see debug messages in TldLocationsCache, uncomment the following line:
+#org.apache.jasper.compiler.TldLocationsCache.level = FINE
+org.apache.catalina.core.ContainerBase.[Catalina].[localhost].level = FINE
+
+## Uncomment this if you would like the system to log messages into stdout
+#log4j.rootLogger=TRACE, rootfile
+#log4j.appender.rootfile=org.apache.log4j.RollingFileAppender
+#log4j.appender.rootfile.File=JABAWSLogFilename.log
+#log4j.appender.rootfile.Target=System.out
+#log4j.appender.rootfile.layout=org.apache.log4j.PatternLayout
+#log4j.appender.rootfile.layout.ConversionPattern=%t %d %m%n
+
+## Uncomment to enable JWS2 activity logging to the file
+#logDir = .
+#log4j.logger.compbio=TRACE, ACTIVITY
+#log4j.appender.ACTIVITY=org.apache.log4j.RollingFileAppender
+################log4j.appender.ACTIVITY.File=${logDir}/activity.log
+#log4j.appender.ACTIVITY.File=${catalina.base}/logs/JABAWSLogFilename.log
+#log4j.appender.ACTIVITY.MaxFileSize=10MB
+#log4j.appender.ACTIVITY.MaxBackupIndex=10000
+#log4j.appender.ACTIVITY.layout=org.apache.log4j.PatternLayout
+#log4j.appender.ACTIVITY.layout.ConversionPattern=%d{MM-dd@HH:mm:ss} %-5p %3x - %m%n
+
+## Uncomment for separate local engine execution log (debugging only)
+#log4j.logger.compbio.engine.local.LocalExecutorService=INFO, C
+#log4j.appender.C=org.apache.log4j.FileAppender
+#log4j.appender.C.File=LocalExecutorService.log
+#log4j.appender.C.layout=org.apache.log4j.PatternLayout
+#log4j.appender.C.layout.ConversionPattern=%m%n
+
+##################################################################################################################################
+#log4j.appender.stdout=org.apache.log4j.ConsoleAppender
+#log4j.appender.stdout.Target=System.out
+#log4j.appender.stdout.layout=org.apache.log4j.PatternLayout
+#log4j.appender.stdout.layout.ConversionPattern=%m%n
+#log4j.rootLogger=info, stdout
+
+log4j.rootLogger=ERROR, R
+log4j.appender.R=org.apache.log4j.FileAppender
+log4j.appender.R.File=${catalina.base}/logs/errors.log
+log4j.appender.R.layout=org.apache.log4j.PatternLayout
+log4j.appender.R.layout.ConversionPattern=%m%n %d{MM-dd@HH:mm:ss} %-5p (%13F:%L) %3x - 
+
+# %d{ABSOLUTE} %5p %c{1}:%L -
+log4j.logger.compbio=DEBIG, B
+log4j.appender.B=org.apache.log4j.FileAppender
+log4j.appender.B.File=${catalina.base}/logs/debugging.log
+log4j.appender.B.layout=org.apache.log4j.PatternLayout
+log4j.appender.B.layout.ConversionPattern=%m%n %d{MM-dd@HH:mm:ss} %-5p (%13F:%L) %3x - 
+
+# %d{ABSOLUTE} %5p %c{1}:%L -
+#log4j.logger.compbio.engine.local.LocalExecutorService=INFO, C
+#log4j.appender.C=org.apache.log4j.FileAppender
+#log4j.appender.C.File=LocalExecutorService.log
+#log4j.appender.C.layout=org.apache.log4j.PatternLayout
+#log4j.appender.C.layout.ConversionPattern=%m%n
+# %d{MM-dd@HH:mm:ss} %-5p (%13F:%L) %3x - 
diff --git a/src/main/website/AllReports.jsp b/src/main/website/AllReports.jsp
new file mode 100644
index 0000000..ea597a9
--- /dev/null
+++ b/src/main/website/AllReports.jsp
@@ -0,0 +1,11 @@
+<%
+	String query = request.getParameter("query");
+	if (query.equals("date"))
+		response.sendRedirect("QueryJobsByDate.jsp");
+	else if (query.equals("length"))
+		response.sendRedirect("QueryTimeExecition.jsp");
+	else if (query.equals("protein"))
+		response.sendRedirect("QuerySequenceProtein.jsp");
+	else if (query.equals("log"))
+		response.sendRedirect("QueryLogInfo.jsp");
+%>
\ No newline at end of file
diff --git a/src/main/website/Index.jsp b/src/main/website/Index.jsp
new file mode 100644
index 0000000..56f3a6b
--- /dev/null
+++ b/src/main/website/Index.jsp
@@ -0,0 +1,19 @@
+<%@ page language="java" contentType="text/html; charset=UTF-8"
+    pageEncoding="UTF-8"%>
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<html>
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<title>Cassandra report</title>
+</head>
+<body>
+	<form method="post" action="AllReports.jsp">
+		<h3>Choose query type</h3>
+		<input type="radio" name="query" value="protein" Checked>Search by protein sequence<br/>
+		<input type="radio" name="query" value="date">Search by date<br/>
+		<input type="radio" name="query" value="log">Log information for current job<br/>		
+		<input type="radio" name="query" value="length">Usage statistics by job time execution<br/>	
+		<input type="submit" name="Search" value="Search"/>
+	</form>
+</body>
+</html>
\ No newline at end of file
diff --git a/src/main/website/PrintResult.jsp b/src/main/website/PrintResult.jsp
new file mode 100644
index 0000000..c2f2e81
--- /dev/null
+++ b/src/main/website/PrintResult.jsp
@@ -0,0 +1,21 @@
+<%@ page language="java" contentType="text/html; charset=UTF-8"
+    pageEncoding="UTF-8"%>
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<html>
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<title>Report</title>
+</head>
+<body>
+<h3>Report Results</h3> 
+<% 	String rez = request.getAttribute("result").toString();
+	String[] rezLines = rez.split(";");
+	for (int i = 0; i < rezLines.length; i++) {
+%>
+<%= rezLines[i]+"<br/>" %>
+<%
+}
+%>
+<a href="javascript:history.back()">Click here to go Back</a>
+</body>
+</html>
\ No newline at end of file
diff --git a/src/main/website/QueryJobsByDate.jsp b/src/main/website/QueryJobsByDate.jsp
new file mode 100644
index 0000000..ae667fd
--- /dev/null
+++ b/src/main/website/QueryJobsByDate.jsp
@@ -0,0 +1,24 @@
+<%@ page language="java" contentType="text/html; charset=UTF-8"
+    pageEncoding="UTF-8"%>
+    <%@page import="java.util.Calendar"%>
+   
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<html>
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<title>Date period</title>
+</head>
+<body>
+	<form method="post" action="ServletJobsByDate">
+		<h3>Enter time period</h3>	
+		 <% Calendar cal = Calendar.getInstance();
+			String datecalBegin = cal.get(Calendar.YEAR) + "/" + (cal.get(Calendar.MONTH) + 1) + "/1";
+			String datecalEnd = cal.get(Calendar.YEAR) + "/" + (cal.get(Calendar.MONTH) + 1) + "/" + cal.get(Calendar.DAY_OF_MONTH);
+		 %>
+		<p>from  <input type="text" name="data1" value = <%= datecalBegin%> style=" width : 145px;"/>
+		to <input type="text" name="data2" value = <%= datecalEnd%> style=" width : 145px;"/></p>
+		<input type="checkbox" name="option" value="AllDate">Query for all dates<br>
+		<input type="submit" name="Search" value="Search"/>
+	</form>
+</body>
+</html>
\ No newline at end of file
diff --git a/src/main/website/QueryLogInfo.jsp b/src/main/website/QueryLogInfo.jsp
new file mode 100644
index 0000000..34f0f9f
--- /dev/null
+++ b/src/main/website/QueryLogInfo.jsp
@@ -0,0 +1,17 @@
+<%@ page language="java" contentType="text/html; charset=UTF-8"
+    pageEncoding="UTF-8"%>
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<html>
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<title>Log query</title>
+</head>
+<body>
+	<br/>
+	<form method="get" action="ServletLogInfo">
+		<h3>Enter job ID</h3>	
+		<input type="text" name="IdJob"><br/>
+		<input type="submit" name="Search" value="Search"/><br/><br/>
+	</form>
+</body>
+</html>
\ No newline at end of file
diff --git a/src/main/website/QuerySequenceProtein.jsp b/src/main/website/QuerySequenceProtein.jsp
new file mode 100644
index 0000000..3d86bd6
--- /dev/null
+++ b/src/main/website/QuerySequenceProtein.jsp
@@ -0,0 +1,23 @@
+<%@ page language="java" contentType="text/html; charset=UTF-8"
+    pageEncoding="UTF-8"%>
+   
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<html>
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<title>Sequence of protein</title>
+</head>
+<body>
+	<br/>
+	<form method="get" action="ServletSequenceProtein">
+		<h3>Enter protein sequence</h3>	
+		<p><textarea rows="14" cols="80" name="prot">ABCDE</textarea></p>
+		<input type="radio" name="protein" value="whole" Checked>search whole<br/>
+		<input type="radio" name="protein" value="part">search part<br/>
+		<input type="submit" name="Search" value="Search sequence"/><br/><br/>
+		<h3>Enter minimum number of jobs per protein</h3>
+		<input type="text" name="counterJob" value = 3><br/>
+		<input type="submit" name="Search" value="Search counter"/><br/><br/>
+	</form>
+</body>
+</html>
diff --git a/src/main/website/QueryTimeExecition.jsp b/src/main/website/QueryTimeExecition.jsp
new file mode 100644
index 0000000..aaf925f
--- /dev/null
+++ b/src/main/website/QueryTimeExecition.jsp
@@ -0,0 +1,28 @@
+<%@ page language="java" contentType="text/html; charset=UTF-8"
+	pageEncoding="UTF-8"%>
+<%@page import="java.util.Calendar"%>
+
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<html>
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<title>Date interval</title>
+</head>
+<body>
+	<form method="post" action="ServletTimeExecution">
+		<h3>Enter time period</h3>
+		<%
+			Calendar cal = Calendar.getInstance();
+			String datecalBegin = cal.get(Calendar.YEAR) + "/" + cal.get(Calendar.MONTH) + "/" + cal.get(Calendar.DAY_OF_MONTH);
+			String datecalEnd = cal.get(Calendar.YEAR) + "/" + (cal.get(Calendar.MONTH) + 1) + "/" + cal.get(Calendar.DAY_OF_MONTH);
+		%>
+		<p>
+			from <input type="text" name="data1" value=<%=datecalBegin%>
+				style="width: 145px;" /> to <input type="text" name="data2"
+				value=<%=datecalEnd%> style="width: 145px;" />
+		</p>
+		<input type="checkbox" name="option" value="AllDate">Query for
+		all dates<br> <input type="submit" name="Search" value="Search" />
+	</form>
+</body>
+</html>
diff --git a/src/main/website/ReportJobsByDate.jsp b/src/main/website/ReportJobsByDate.jsp
new file mode 100644
index 0000000..261a11b
--- /dev/null
+++ b/src/main/website/ReportJobsByDate.jsp
@@ -0,0 +1,62 @@
+<%@page import="java.util.ArrayList"%>
+<%@ taglib uri="http://java.sun.com/jsp/jstl/core" prefix="c"%>
+<%@ taglib uri="http://java.sun.com/jsp/jstl/functions" prefix="fn"%>
+<%@ taglib uri="http://java.sun.com/jsp/jstl/fmt" prefix="fmt"%>
+<%@ taglib uri="http://displaytag.sf.net" prefix="dt"%>
+<c:choose>
+	<c:when test="${flag == 'AllDate'}">
+		<h3>Jobs statistics for the whole period</h3>
+	</c:when>
+	<c:otherwise>
+		<h3>
+			Jobs statistics for the Period:
+			<c:out value="${data1}" />
+			to
+			<c:out value="${data2}" />
+		</h3>
+	</c:otherwise>
+</c:choose>
+<h3>Time execution: ${timeExecution} ms</h3>
+
+<c:set var="sum" value="0" />
+<c:forEach items="${result}" var="res">
+	<c:set var="tot" value="${res.total}" />
+	<c:set var="sum" value="${sum + tot}" />
+</c:forEach>
+
+
+<table border="1" style="border-collapse: collapse; white-space: nowrap">
+	<thead>
+		<tr>
+			<th rowspan="2" style="text-align: centre">Date</th>
+			<th colspan="4" style="text-align: centre">Number of Proteins</th>
+		</tr>
+		<tr>
+			<th style="text-align: centre">Total</th>
+			<th style="text-align: centre">Failed</th>
+			<th style="text-align: centre">Cancelled</th>
+			<th style="text-align: centre">Abandoned</th>
+		</tr>
+	</thead>
+	<tbody>
+
+		<tr style="font-weight: bolder;">
+			<td>Total:</td>
+			<td style="text-align: right">${sum}</td>
+			<td style="text-align: right">0</td>
+			<td style="text-align: right">0</td>
+			<td style="text-align: right">0</td>
+		</tr>
+
+		<c:forEach items="${result}" var="res">
+			<tr>
+				<td>${res.date}</td>
+				<td style="text-align: right"><c:out value="${res.total}" /></td>
+				<td style="text-align: right">0</td>
+				<td style="text-align: right">0</td>
+				<td style="text-align: right">0</td>
+			</tr>
+		</c:forEach>
+
+	</tbody>
+</table>
\ No newline at end of file
diff --git a/src/main/website/ReportLogInfo.jsp b/src/main/website/ReportLogInfo.jsp
new file mode 100644
index 0000000..97ec1f3
--- /dev/null
+++ b/src/main/website/ReportLogInfo.jsp
@@ -0,0 +1,24 @@
+<%@page import="java.util.ArrayList"%>
+<%@ taglib uri="http://java.sun.com/jsp/jstl/core" prefix="c" %>
+<%@ taglib uri="http://java.sun.com/jsp/jstl/functions" prefix="fn" %>
+<%@ taglib uri="http://java.sun.com/jsp/jstl/fmt" prefix="fmt" %>
+<%@ taglib uri="http://displaytag.sf.net" prefix="dt" %>
+<h3>Jobs log information for: ${IdJob}</h3>
+<h3>Time execution: ${timeExecution} ms</h3>
+<p> Date Start : ${result.logInfo.dateStart}<br/>
+ Date End   : ${result.logInfo.dateEnd}<br/>
+ IP            : ${result.logInfo.ip}</p>
+<table border="1" style="border-collapse: collapse; white-space: nowrap">
+<tbody>
+<tr>
+<td> Sequence</td>
+<td style="text-align: left; border-buttom: dotted; font-family: monospace"> ${result.logInfo.sequence}</td>
+</tr>
+<c:forEach items="${result.logInfo.prediction}" var="pred">
+<tr>
+	<td> ${pred.key}</td>
+	<td style="text-align: left; border-buttom: dotted; font-family: monospace"> ${pred.value}</td>
+</tr>
+</c:forEach>
+</tbody>
+</table>
diff --git a/src/main/website/ReportSequenceProtein.jsp b/src/main/website/ReportSequenceProtein.jsp
new file mode 100644
index 0000000..0459668
--- /dev/null
+++ b/src/main/website/ReportSequenceProtein.jsp
@@ -0,0 +1,76 @@
+<%@page import="java.util.ArrayList"%>
+<%@ page trimDirectiveWhitespaces="true"%>
+<%@ taglib uri="http://java.sun.com/jsp/jstl/core" prefix="c"%>
+<%@ taglib uri="http://java.sun.com/jsp/jstl/functions" prefix="fn"%>
+<%@ taglib uri="http://java.sun.com/jsp/jstl/fmt" prefix="fmt"%>
+<%@ taglib uri="http://displaytag.sf.net" prefix="dt"%>
+<c:choose>
+	<c:when test="${search == 'Search counter'}">
+		<h3>Dundee ProteoCache query result for jobs more than ${counter} </h3>
+	</c:when>
+	<c:otherwise>
+		<h3>Dundee ProteoCache query result</h3>
+	</c:otherwise>
+</c:choose>
+<h3>Time execution: ${timeExecution} ms</h3>
+<table border="1" style="border-collapse: collapse; white-space: nowrap">
+	<c:choose>
+		<c:when test="${search == 'Search counter'}">
+			<thead>
+				<tr>
+					<th style="text-align: centre">Number of jobs</th>
+					<th style="text-align: left">Protein</th>
+				</tr>
+			</thead>
+			<tbody>
+				<c:forEach items="${result}" var="res">
+					<tr>
+						<td>${res.totalId}</td>
+						<td
+							style="text-align: left; border-buttom: dotted; font-family: monospace"><a
+							title="Click to view predictions"
+							href="ServletSequenceProtein?prot=${res.prot}&protein=whole&Search=Search+sequence&counterJob=${counter}">${res.prot}</a>
+						</td>
+					</tr>
+				</c:forEach>
+		</c:when>
+		<c:otherwise>
+			<thead>
+				<tr>
+					<th style="text-align: centre">ID</th>
+					<th style="text-align: centre">Prediction</th>
+				</tr>
+			</thead>
+			<tbody>
+				<c:forEach items="${result}" var="res" varStatus="status">
+					<tr>
+						<td rowspan="2">${res.id}</td>
+						<c:if test="${flag == 'whole'}">
+							<td
+								style="text-align: left; border-buttom: dotted; font-family: monospace"><c:out
+									value="${res.prot}" /></td>
+						</c:if>
+						<c:if test="${flag == 'part'}">
+							<td
+								style="text-align: left; border-buttom: dotted; font-family: monospace">
+								<c:forEach items="${res.subProt}" var="seq">
+									<c:choose>
+										<c:when test="${fn:contains(seq, prot)}">
+											<span style="background-color: blue">${seq}</span>
+										</c:when>
+										<c:otherwise>${seq}</c:otherwise>
+									</c:choose>
+								</c:forEach>
+							</td>
+						</c:if>
+					</tr>
+					<tr>
+						<td
+							style="text-align: left; border-top: hidden; font-family: monospace"><c:out
+								value="${res.jpred}" /></td>
+					</tr>
+				</c:forEach>
+		</c:otherwise>
+	</c:choose>
+	</tbody>
+</table>
diff --git a/src/main/website/ReportTimeExecution.jsp b/src/main/website/ReportTimeExecution.jsp
new file mode 100644
index 0000000..e68dc64
--- /dev/null
+++ b/src/main/website/ReportTimeExecution.jsp
@@ -0,0 +1,68 @@
+<%@page import="java.util.ArrayList"%>
+<%@ page trimDirectiveWhitespaces="true"%>
+<%@ taglib uri="http://java.sun.com/jsp/jstl/core" prefix="c"%>
+<%@ taglib uri="http://java.sun.com/jsp/jstl/functions" prefix="fn"%>
+<%@ taglib uri="http://java.sun.com/jsp/jstl/fmt" prefix="fmt"%>
+<%@ taglib uri="http://displaytag.sf.net" prefix="dt"%>
+<c:choose>
+	<c:when test="${flag == 'AllDate'}">
+		<h3>Time execution for the whole period</h3>
+	</c:when>
+	<c:otherwise>
+		<h3>Time execution for the interval: ${data1} - ${data2}</h3>
+	</c:otherwise>
+</c:choose>
+<h3>Time execution: ${timeExecution} ms</h3>
+
+<c:set var="sum" value="0" />
+<c:forEach items="${result}" var="res" varStatus="loop">
+	<c:choose>
+		<c:when test="${loop.last}">
+			<c:forEach items="${res.timeTotalExec}" var="total">
+				<c:set var="sum" value="${sum + total}" />
+			</c:forEach>
+		</c:when>
+	</c:choose>
+</c:forEach>
+
+<h3>Total number of jobs: ${sum}</h3>
+
+<table border="1" style="border-collapse: collapse; white-space: nowrap">
+	<thead>
+		<tr>
+			<th style="text-align: centre; width: 150px">Date</th>
+			<th style="text-align: centre; width: 150px">less then 30 s</th>
+			<th style="text-align: centre; width: 150px">30 s - 60 s</th>
+			<th style="text-align: centre; width: 150px">1 min - 2 min</th>
+			<th style="text-align: centre; width: 150px">2 min - 10 min</th>
+			<th style="text-align: centre; width: 150px">more then 10 min</th>
+		</tr>
+	</thead>
+	<tbody>
+		<c:forEach items="${result}" var="res" varStatus="loop">
+			<c:choose>
+				<c:when test="${loop.last}">
+					<tr style="font-weight: bolder;">
+						<td>Total:</td>
+						<c:forEach items="${res.timeTotalExec}" var="total">
+							<td style="text-align: right">${total}</td>
+						</c:forEach>
+					</tr>
+				</c:when>
+			</c:choose>
+		</c:forEach>
+
+		<c:forEach items="${result}" var="res" varStatus="loop">
+			<c:choose>
+				<c:when test="${not loop.last}">
+					<tr>
+						<td>${res.date}</td>
+						<c:forEach items="${res.timeRez}" var="time">
+							<td style="text-align: right">${time}</td>
+						</c:forEach>
+					</tr>
+				</c:when>
+			</c:choose>
+		</c:forEach>
+	</tbody>
+</table>
diff --git a/src/main/website/StatisticsProtein.jsp b/src/main/website/StatisticsProtein.jsp
new file mode 100644
index 0000000..06c7d72
--- /dev/null
+++ b/src/main/website/StatisticsProtein.jsp
@@ -0,0 +1,41 @@
+<%@ taglib uri="http://java.sun.com/jsp/jstl/core" prefix="c" %>
+<%@ taglib uri="http://java.sun.com/jsp/jstl/functions" prefix="fn" %>
+<%@ taglib uri="http://java.sun.com/jsp/jstl/fmt" prefix="fmt" %>
+<%@ taglib uri="http://displaytag.sf.net" prefix="dt" %>
+
+<table class="its" style="width:800px" border="1"> 
+<thead>
+<tr>
+<th rowspan="2"style="text-align: centre">Date</th>
+<th colspan="4" style="text-align: centre">Number of Proteins</th>
+</tr>
+<tr>
+<th style="text-align: centre">Total</th>
+<th style="text-align: centre">Failed</th>
+<th style="text-align: centre">Cancelled</th>
+<th style="text-align: centre">Abandoned</th>
+</tr>
+</thead>
+<tbody>
+<c:set var="sum"  value="0" />
+<c:forEach items="${statistics}" var="res">
+<tr>
+<td>${res.date}</td>
+<c:set var="tot"  value="${res.total}" />
+<c:set var="sum"  value="${sum + tot}" />
+<td style="text-align: right"><c:out value = "${res.total}" /></td>
+<td style="text-align: right">0</td>
+<td style="text-align: right">0</td>
+<td style="text-align: right">0</td>
+</tr>
+</c:forEach>
+<tr style="font-weight: bolder;">
+<td>Total:</td>
+<td style="text-align: right">${sum}</td>
+<td style="text-align: right">0</td>
+<td style="text-align: right">0</td>
+<td style="text-align: right">0</td>
+
+</tr>
+</tbody>
+</table>
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diff --git a/src/main/website/WEB-INF/lib/netty-3.6.6.Final.jar b/src/main/website/WEB-INF/lib/netty-3.6.6.Final.jar
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diff --git a/src/main/website/WEB-INF/lib/slf4j-api-1.7.5.jar b/src/main/website/WEB-INF/lib/slf4j-api-1.7.5.jar
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diff --git a/src/main/website/WEB-INF/lib/slf4j-simple-1.7.5.jar b/src/main/website/WEB-INF/lib/slf4j-simple-1.7.5.jar
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diff --git a/src/main/website/WEB-INF/lib/snappy-java-1.1.0.jar b/src/main/website/WEB-INF/lib/snappy-java-1.1.0.jar
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diff --git a/src/main/website/WEB-INF/web.xml b/src/main/website/WEB-INF/web.xml
new file mode 100644
index 0000000..242a900
--- /dev/null
+++ b/src/main/website/WEB-INF/web.xml
@@ -0,0 +1,360 @@
+<web-app xmlns="http://java.sun.com/xml/ns/j2ee"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://java.sun.com/xml/ns/j2ee http://java.sun.com/xml/ns/j2ee/web-app_2_4.xsd"
+ version="2.4">
+
+<display-name>ProteoCache</display-name>
+<description>ProteoCache - Results repository for the Dundee Resource</description>
+
+	<welcome-file-list>
+		<welcome-file>Index.jsp</welcome-file>
+	</welcome-file-list>
+
+	<!-- ProteoCache listeners -->
+	<listener>
+		<listener-class>compbio.listeners.ContextListener</listener-class>
+	</listener>
+
+
+	<!-- Session timeout in minutes -->
+	<session-config>
+		<session-timeout>20</session-timeout>
+	</session-config>
+
+
+	<servlet>
+		<display-name>This is a standard tomcat 'default' servlet for making listings</display-name>
+		<servlet-name>listings</servlet-name>
+		<servlet-class>org.apache.catalina.servlets.DefaultServlet</servlet-class>
+		<init-param>
+			<param-name>debug</param-name>
+			<param-value>0</param-value>
+		</init-param>
+		<init-param>
+			<param-name>readonly</param-name>
+			<param-value>true</param-value>
+		</init-param>
+		<init-param>
+			<param-name>listings</param-name>
+			<param-value>true</param-value>
+		</init-param>
+		<load-on-startup>1</load-on-startup>
+	</servlet>
+
+
+	<!-- ProteoCache servlets -->
+<!--
+	<servlet>
+		<description>Display pre-calculated accounting info</description>
+		<servlet-name>DisplayStat</servlet-name>
+		<servlet-class>compbio.stat.servlet.DisplayStat</servlet-class>
+	</servlet>
+
+	<servlet>
+		<description>WebServices Status</description>
+		<servlet-name>ServiceStatus</servlet-name>
+		<servlet-class>compbio.stat.servlet.ServiceStatus</servlet-class>
+	</servlet>
+
+	<servlet>
+		<servlet-name>DownloadRedirector</servlet-name>
+		<servlet-class>compbio.stat.servlet.DownloadRedirector</servlet-class>
+	</servlet>
+
+	<servlet>
+		<description>WebService Status with no UI. Accepts web service name as a parameter</description>
+		<servlet-name>HttpCodeResponseServiceStatus</servlet-name>
+		<servlet-class>compbio.stat.servlet.HttpCodeResponseServiceStatus</servlet-class>
+	</servlet>
+
+	<servlet>
+		<description>Display job list</description>
+		<servlet-name>Joblist</servlet-name>
+		<servlet-class>compbio.stat.servlet.Joblist</servlet-class>
+	</servlet>
+
+	<servlet>
+		<description>Display monthly summary statistics</description>
+		<servlet-name>AnnualStat</servlet-name>
+		<servlet-class>compbio.stat.servlet.AnnualStat</servlet-class>
+	</servlet>
+
+	<servlet>
+		<description>Display monthly summary statistics with no links to details</description>
+		<servlet-name>PublicAnnualStat</servlet-name>
+		<servlet-class>compbio.stat.servlet.AnnualStat</servlet-class>
+	</servlet>
+
+	<servlet>
+		<servlet-name>RegistryWS</servlet-name>
+		<servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
+		<load-on-startup>1</load-on-startup>
+	</servlet>
+
+	<servlet>
+		<servlet-name>ClustalWS</servlet-name>
+		<servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
+		<load-on-startup>1</load-on-startup>
+	</servlet>
+
+	<servlet>
+		<servlet-name>ClustalOWS</servlet-name>
+		<servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
+		<load-on-startup>1</load-on-startup>
+	</servlet>
+
+	<servlet>
+		<servlet-name>MuscleWS</servlet-name>
+		<servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
+		<load-on-startup>1</load-on-startup>
+	</servlet>
+
+	<servlet>
+		<servlet-name>MafftWS</servlet-name>
+		<servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
+		<load-on-startup>1</load-on-startup>
+	</servlet>
+
+	<servlet>
+		<servlet-name>TcoffeeWS</servlet-name>
+		<servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
+		<load-on-startup>1</load-on-startup>
+	</servlet>
+
+	<servlet>
+		<servlet-name>ProbconsWS</servlet-name>
+		<servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
+		<load-on-startup>1</load-on-startup>
+	</servlet>
+
+	<servlet>
+		<servlet-name>MSAprobsWS</servlet-name>
+		<servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
+		<load-on-startup>1</load-on-startup>
+	</servlet>
+
+	<servlet>
+		<servlet-name>GLprobsWS</servlet-name>
+		<servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
+		<load-on-startup>1</load-on-startup>
+	</servlet>
+
+	<servlet>
+		<servlet-name>AAConWS</servlet-name>
+		<servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
+		<load-on-startup>1</load-on-startup>
+	</servlet>
+
+	<servlet>
+		<servlet-name>JronnWS</servlet-name>
+		<servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
+		<load-on-startup>1</load-on-startup>
+	</servlet>
+
+	<servlet>
+		<servlet-name>DisemblWS</servlet-name>
+		<servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
+		<load-on-startup>1</load-on-startup>
+	</servlet>
+
+	<servlet>
+		<servlet-name>GlobPlotWS</servlet-name>
+		<servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
+		<load-on-startup>1</load-on-startup>
+	</servlet>
+
+	<servlet>
+		<servlet-name>IUPredWS</servlet-name>
+		<servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
+		<load-on-startup>1</load-on-startup>
+	</servlet>
+
+	<servlet>
+		<servlet-name>JpredWS</servlet-name>
+		<servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
+		<load-on-startup>1</load-on-startup>
+	</servlet>
+	<servlet>
+		<servlet-name>RNAalifoldWS</servlet-name>
+		<servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
+		<load-on-startup>1</load-on-startup>
+	</servlet>
+-->
+
+
+
+	<!-- ProteoCache servlet mappings -->
+<!--
+	<servlet-mapping>
+		<servlet-name>listings</servlet-name>
+		<url-pattern>/</url-pattern>
+	</servlet-mapping>
+
+	<servlet-mapping>
+		<servlet-name>DownloadRedirector</servlet-name>
+		<url-pattern>/download</url-pattern>
+	</servlet-mapping>
+
+	<servlet-mapping>
+		<servlet-name>DisplayStat</servlet-name>
+		<url-pattern>/DisplayStat</url-pattern>
+	</servlet-mapping>
+
+	<servlet-mapping>
+		<servlet-name>ServiceStatus</servlet-name>
+		<url-pattern>/ServiceStatus</url-pattern>
+	</servlet-mapping>
+
+	<servlet-mapping>
+		<servlet-name>HttpCodeResponseServiceStatus</servlet-name>
+		<url-pattern>/HttpCodeResponseServiceStatus/*</url-pattern>
+	</servlet-mapping>
+
+	<servlet-mapping>
+		<servlet-name>AnnualStat</servlet-name>
+		<url-pattern>/AnnualStat</url-pattern>
+	</servlet-mapping>
+
+	<servlet-mapping>
+		<servlet-name>PublicAnnualStat</servlet-name>
+		<url-pattern>/PublicAnnualStat</url-pattern>
+	</servlet-mapping>
+
+	<servlet-mapping>
+		<servlet-name>Joblist</servlet-name>
+		<url-pattern>/Joblist</url-pattern>
+	</servlet-mapping>
+
+	<servlet-mapping>
+		<servlet-name>RegistryWS</servlet-name>
+		<url-pattern>/RegistryWS</url-pattern>
+	</servlet-mapping>
+
+	<servlet-mapping>
+		<servlet-name>ClustalWS</servlet-name>
+		<url-pattern>/ClustalWS</url-pattern>
+	</servlet-mapping>
+
+	<servlet-mapping>
+		<servlet-name>ClustalOWS</servlet-name>
+		<url-pattern>/ClustalOWS</url-pattern>
+	</servlet-mapping>
+
+	<servlet-mapping>
+		<servlet-name>MuscleWS</servlet-name>
+		<url-pattern>/MuscleWS</url-pattern>
+	</servlet-mapping>
+
+	<servlet-mapping>
+		<servlet-name>MafftWS</servlet-name>
+		<url-pattern>/MafftWS</url-pattern>
+	</servlet-mapping>
+
+	<servlet-mapping>
+		<servlet-name>TcoffeeWS</servlet-name>
+		<url-pattern>/TcoffeeWS</url-pattern>
+	</servlet-mapping>
+
+	<servlet-mapping>
+		<servlet-name>ProbconsWS</servlet-name>
+		<url-pattern>/ProbconsWS</url-pattern>
+	</servlet-mapping>
+
+	<servlet-mapping>
+		<servlet-name>MSAprobsWS</servlet-name>
+		<url-pattern>/MSAprobsWS</url-pattern>
+	</servlet-mapping>
+
+	<servlet-mapping>
+		<servlet-name>GLprobsWS</servlet-name>
+		<url-pattern>/GLprobsWS</url-pattern>
+	</servlet-mapping>
+
+	<servlet-mapping>
+		<servlet-name>AAConWS</servlet-name>
+		<url-pattern>/AAConWS</url-pattern>
+	</servlet-mapping>
+
+	<servlet-mapping>
+		<servlet-name>JronnWS</servlet-name>
+		<url-pattern>/JronnWS</url-pattern>
+	</servlet-mapping>
+
+	<servlet-mapping>
+		<servlet-name>DisemblWS</servlet-name>
+		<url-pattern>/DisemblWS</url-pattern>
+	</servlet-mapping>
+
+	<servlet-mapping>
+		<servlet-name>GlobPlotWS</servlet-name>
+		<url-pattern>/GlobPlotWS</url-pattern>
+	</servlet-mapping>
+
+	<servlet-mapping>
+		<servlet-name>IUPredWS</servlet-name>
+		<url-pattern>/IUPredWS</url-pattern>
+	</servlet-mapping>
+
+	<servlet-mapping>
+		<servlet-name>JpredWS</servlet-name>
+		<url-pattern>/JpredWS</url-pattern>
+	</servlet-mapping>
+
+	<servlet-mapping>
+		<servlet-name>RNAalifoldWS</servlet-name>
+		<url-pattern>/RNAalifoldWS</url-pattern>
+	</servlet-mapping>
+-->
+
+
+	<!-- ProteoCache security constraints -->
+	<security-constraint>
+		<web-resource-collection>
+		<web-resource-name>Administrator pages</web-resource-name>
+			<!-- Prohibit access to any resources -->
+			<url-pattern>/DisplayStat</url-pattern>
+			<url-pattern>/Joblist</url-pattern>
+			<url-pattern>/AnnualStat</url-pattern>
+			<url-pattern>/conf/*</url-pattern>
+			<url-pattern>/binaries/*</url-pattern>
+			<url-pattern>/testsrc/*</url-pattern>
+			<url-pattern>/lib/*</url-pattern>
+			<!-- Uncomment this to secure services status checker 
+			<url-pattern>/HttpCodeResponseServiceStatus/*</url-pattern>
+			<url-pattern>/ServiceStatus</url-pattern>
+			-->
+			<!-- No http-method means all methods are constrained -->
+		</web-resource-collection>
+		<auth-constraint>
+			<role-name>admin</role-name>
+		</auth-constraint>
+	</security-constraint>
+
+
+	<!-- unsupported HTTP methods -->
+	<security-constraint>
+		<web-resource-collection>
+			<web-resource-name>unsupported HTTP methods</web-resource-name>
+			<url-pattern>/*</url-pattern>
+			<http-method>PUT</http-method>
+			<http-method>DELETE</http-method>
+			<http-method>TRACE</http-method>
+			<http-method>OPTIONS</http-method>
+		</web-resource-collection>
+		<auth-constraint/>
+	</security-constraint>
+
+	<!-- Define the Login Configuration for this Application -->
+	<login-config>
+		<auth-method>BASIC</auth-method>
+		<realm-name>ProteCache administrators</realm-name>
+	</login-config>
+
+
+	<!-- Security roles referenced by this web application -->
+	<security-role>
+		<description>The role that is required to log in and view ProteCache internals</description>
+		<role-name>admin</role-name>
+	</security-role>
+
+</web-app>
diff --git a/src/main/website/conf/Engine.properties b/src/main/website/conf/Engine.properties
new file mode 100644
index 0000000..dd2a0db
--- /dev/null
+++ b/src/main/website/conf/Engine.properties
@@ -0,0 +1,38 @@
+#################################################################################
+# enable or disable engine true | false
+# OPTIONAL defaults to true
+engine.local.enable=true 
+
+#################################################################################
+# Directory to use for temporary files storage
+# OPTIONAL defaults to java temporary directory 
+# Relative path within the project will be converted in absolute at runtime
+#local.tmp.directory=/cluster/gjb_lab/fc/www-jws2/jaba/local_jobsout 
+local.tmp.directory=jobsout 
+
+#################################################################################
+# Number of threads for tasks execution (valid values between 1 and 2x cpu. 
+# Where x is a number of cores available in the system)
+# OPTIONAL defaults to the number of cores for core number <=4 and 
+# number of cores-1 for greater core numbers
+engine.local.thread.number=2
+
+#################################################################################
+# Enable/disable cluster statistics collector
+local.stat.collector.enable=true
+# Frequency of statistics collecting (in minutes)
+# normal rate: once a date = 24 * 60 = 1440
+local.stat.collector.update.frequency=1
+
+# Maximum amount of time the job is considered running in hours
+# Optional defaults to 24 hours
+local.stat.maxruntime=6
+
+#################################################################################
+# Maximum amount of time the job directory is living (in hours), 
+# -1 means the directories are never deleted
+# Defaults is one week, i.e. 168 hours
+local.jobdir.maxlifespan=168
+# Frequency of cleaning job directory (in minutes)
+# normal rate: once a date = 24 * 60 = 1440
+local.jobdir.cleaning.frequency=1
diff --git a/src/main/website/conf/GA.properties b/src/main/website/conf/GA.properties
new file mode 100644
index 0000000..904765c
--- /dev/null
+++ b/src/main/website/conf/GA.properties
@@ -0,0 +1,19 @@
+# This file contains settings for Google Analytics (GA) Statistics Engine.
+# Feel free to remove/delete this file if you do not want us to see that you
+# use ProteoCache. 
+# However, we would appreciate it greatly if you could leave it on. ProteoCache 
+# usage statistics are collected for funding and reporting purposes, and no 
+# private information is collected. The data sent by ProteoCache is as follows: 
+# 1) The IP address of the ProteoCache server machine.
+# 2) The name of the web service that was called.
+# 3) A few details of the system such as java version, user language, 
+#    color depth, screen, resolution and character encoding.
+
+# All calls to GA are completed asynchronously and create very little
+# overhead. Thus they do not influence the server response time or performance.
+
+# Values yes or true = enable GA, any other value will disable it
+enable.ga=no
+# If set to yes replaces your server name/IP address with 127.0.0.1
+anonymize.ip=no
+
diff --git a/src/main/website/conf/Proteocache.properties b/src/main/website/conf/Proteocache.properties
new file mode 100644
index 0000000..ae10be4
--- /dev/null
+++ b/src/main/website/conf/Proteocache.properties
@@ -0,0 +1,28 @@
+#################################################################################
+# Cassandra host or IP
+# test server is 10.0.115.190
+cassandra.host=localhost
+
+cassandra.newtables.update=false
+
+#################################################################################
+# Jpred sources
+# real Jpred web-server
+cassandra.jpred.web.update=true
+cassandra.jpred.web.inidelay=0
+cassandra.jpred.web.updaterate=30
+
+# update time period (in days)
+# by defauls for 100 past days
+cassandra.jpred.web.period=5
+
+
+#################################################################################
+# local test job source
+cassandra.jpred.local.update=false
+cassandra.jpred.local.inidelay=10
+cassandra.jpred.local.updaterate=200
+
+# update time period (in days)
+# by defauls for 100 past days
+cassandra.jpred.local.period=300