Code for Jpred Job java Bean

diff --git a/engine/compbio/engine/Job.java b/engine/compbio/engine/Job.java
new file mode 100644 (file)
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 (file)
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;
+       }
+}