From ada58be75fc7cd59e09bf79568233430a86db8f1 Mon Sep 17 00:00:00 2001
From: Sasha Sherstnev <a.sherstnev@dundee.ac.uk>
Date: Tue, 12 Nov 2013 18:31:30 +0000
Subject: [PATCH] Code for Jpred Job java Bean

---
 engine/compbio/engine/Job.java      |  167 +++++++++++++++++++++++++++++++++++
 engine/compbio/engine/JpredJob.java |   64 ++++++++++++++
 2 files changed, 231 insertions(+)
 create mode 100644 engine/compbio/engine/Job.java
 create mode 100644 engine/compbio/engine/JpredJob.java

diff --git a/engine/compbio/engine/Job.java b/engine/compbio/engine/Job.java
new file mode 100644
index 0000000..309e0e9
--- /dev/null
+++ b/engine/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/engine/compbio/engine/JpredJob.java b/engine/compbio/engine/JpredJob.java
new file mode 100644
index 0000000..a606746
--- /dev/null
+++ b/engine/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;
+	}
+}
-- 
1.7.10.2