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Clean up the code
author
Sasha Sherstnev
<a.sherstnev@dundee.ac.uk>
Mon, 27 Jan 2014 14:53:16 +0000
(14:53 +0000)
committer
Sasha Sherstnev
<a.sherstnev@dundee.ac.uk>
Mon, 27 Jan 2014 14:53:16 +0000
(14:53 +0000)
datadb/compbio/beans/DateBean.java
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datadb/compbio/cassandra/DataBase.java
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datadb/compbio/cassandra/JpredParserLocalFile.java
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engine/compbio/engine/ExecutionInterval.java
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engine/compbio/engine/JpredJob.java
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server/compbio/statistic/CassandraRequester.java
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diff --git
a/datadb/compbio/beans/DateBean.java
b/datadb/compbio/beans/DateBean.java
index
7c593d3
..
b00e1d6
100644
(file)
--- a/
datadb/compbio/beans/DateBean.java
+++ b/
datadb/compbio/beans/DateBean.java
@@
-1,7
+1,6
@@
package compbio.beans;
import java.util.HashMap;
package compbio.beans;
import java.util.HashMap;
-import java.util.LinkedHashMap;
import java.util.Map;
public class DateBean {
import java.util.Map;
public class DateBean {
diff --git
a/datadb/compbio/cassandra/DataBase.java
b/datadb/compbio/cassandra/DataBase.java
index
e741b39
..
6ced180
100644
(file)
--- a/
datadb/compbio/cassandra/DataBase.java
+++ b/
datadb/compbio/cassandra/DataBase.java
@@
-1,8
+1,6
@@
package compbio.cassandra;
import java.util.List;
package compbio.cassandra;
import java.util.List;
-import java.util.ArrayList;
-import java.util.Collections;
import compbio.beans.JobBean;
import compbio.beans.ProteinBean;
import compbio.beans.JobBean;
import compbio.beans.ProteinBean;
diff --git
a/datadb/compbio/cassandra/JpredParserLocalFile.java
b/datadb/compbio/cassandra/JpredParserLocalFile.java
index
e2e5dc9
..
c89fe59
100644
(file)
--- a/
datadb/compbio/cassandra/JpredParserLocalFile.java
+++ b/
datadb/compbio/cassandra/JpredParserLocalFile.java
@@
-2,11
+2,8
@@
package compbio.cassandra;
import java.io.BufferedReader;
import java.io.File;
import java.io.BufferedReader;
import java.io.File;
-import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStreamReader;
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.io.FileInputStream;
import java.text.ParseException;
import java.text.SimpleDateFormat;
@@
-19,7
+16,6
@@
import compbio.data.sequence.FastaReader;
import compbio.data.sequence.FastaSequence;
public class JpredParserLocalFile implements JpredParser {
import compbio.data.sequence.FastaSequence;
public class JpredParserLocalFile implements JpredParser {
- private CassandraWriter cw = new CassandraWriter();
private String dirprefix;
public void setSource(String newsourceprefix) {
private String dirprefix;
public void setSource(String newsourceprefix) {
@@
-75,8
+71,6
@@
public class JpredParserLocalFile implements JpredParser {
if (in.matches(date + ":(.*)jp_[^\\s]+")) {
String[] table = in.split("\\s+");
String starttime = table[0];
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";
String id = table[table.length - 1];
totalcount++;
String confilename = dirprefix + "/" + id + "/" + id + ".concise";
@@
-99,10
+93,8
@@
public class JpredParserLocalFile implements JpredParser {
} else {
SimpleDateFormat formatter = new SimpleDateFormat("yyyy/MM/dd");
String dateInString1 = starttime.substring(0, starttime.indexOf(":"));
} else {
SimpleDateFormat formatter = new SimpleDateFormat("yyyy/MM/dd");
String dateInString1 = starttime.substring(0, starttime.indexOf(":"));
- long insertdate = 0;
try {
Date dat = formatter.parse(dateInString1);
try {
Date dat = formatter.parse(dateInString1);
- insertdate = dat.getTime();
} catch (ParseException e) {
e.printStackTrace();
}
} catch (ParseException e) {
e.printStackTrace();
}
diff --git
a/engine/compbio/engine/ExecutionInterval.java
b/engine/compbio/engine/ExecutionInterval.java
index
9b0bcee
..
79b7cb0
100644
(file)
--- a/
engine/compbio/engine/ExecutionInterval.java
+++ b/
engine/compbio/engine/ExecutionInterval.java
@@
-1,6
+1,5
@@
package compbio.engine;
package compbio.engine;
-import compbio.cassandra.Pair;
/**
/**
diff --git
a/engine/compbio/engine/JpredJob.java
b/engine/compbio/engine/JpredJob.java
index
522ad9f
..
99981e4
100644
(file)
--- a/
engine/compbio/engine/JpredJob.java
+++ b/
engine/compbio/engine/JpredJob.java
@@
-17,7
+17,6
@@
public class JpredJob extends Job {
public JpredJob(String jobid, String date1, String date2) {
super(jobid, date1, date2);
public JpredJob(String jobid, String date1, String date2) {
super(jobid, date1, date2);
- this.protein = protein;
predictions = new ArrayList<FastaSequence>();
alignment = new ArrayList<FastaSequence>();
log = "";
predictions = new ArrayList<FastaSequence>();
alignment = new ArrayList<FastaSequence>();
log = "";
@@
-25,7
+24,6
@@
public class JpredJob extends Job {
public JpredJob(String jobid, String date1, String date2, List<FastaSequence> alignment, List<FastaSequence> predictions) {
super(jobid, date1, date2);
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;
}
this.alignment = alignment;
this.predictions = predictions;
}
diff --git
a/server/compbio/statistic/CassandraRequester.java
b/server/compbio/statistic/CassandraRequester.java
index
ca59844
..
1791c0f
100755
(executable)
--- a/
server/compbio/statistic/CassandraRequester.java
+++ b/
server/compbio/statistic/CassandraRequester.java
@@
-19,8
+19,8
@@
import compbio.beans.UserBean;
import compbio.cassandra.CassandraNativeConnector;
import compbio.cassandra.CassandraReaderOld;
import compbio.cassandra.DataBase;
import compbio.cassandra.CassandraNativeConnector;
import compbio.cassandra.CassandraReaderOld;
import compbio.cassandra.DataBase;
-import compbio.cassandra.Pair;
import compbio.engine.JobStatus;
import compbio.engine.JobStatus;
+import compbio.engine.Pair;
public class CassandraRequester {
private CassandraReaderOld db = new CassandraReaderOld();
public class CassandraRequester {
private CassandraReaderOld db = new CassandraReaderOld();
@@
-112,17
+112,16
@@
public class CassandraRequester {
query.add(db);
}
query.add(db);
}
- /* ???? Very strange code...
- DataBase db = new DataBase();
- db.setTimeTotalExec(totalTime);
- query.add(db);
- */
+ /*
+ * ???? Very strange code... DataBase db = new DataBase();
+ * db.setTimeTotalExec(totalTime); query.add(db);
+ */
return query;
}
/*
* query: total number of jobs for the period from date1 till date2
return query;
}
/*
* query: total number of jobs for the period from date1 till date2
- */
+ */
public TotalJobsStatisticBean countJobs(String date1, String date2) {
/*
* if (null == date1) { date1 = "1970/1/1"; } if (null == date2) { date1
public TotalJobsStatisticBean countJobs(String date1, String date2) {
/*
* if (null == date1) { date1 = "1970/1/1"; } if (null == date2) { date1