}
/*
+ * getting data from the db
+ */
+ public List<Pair<String, String>> ReadProteinData(long day) {
+ final long startTime = System.currentTimeMillis();
+ String com = "SELECT JobID, Protein FROM ProteinData WHERE jobtime = " + day + ";";
+ 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");
+ 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("JobID"), r.getString("Protein"));
+ 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 List<Long> ReadDateTable(long queryDate) {
/*
* getting whole protein sequence from the db ProteinRow
*/
- public List<StructureProteinPrediction> ReadWholeSequence(String queryProtein) {
+ public List<AnnotatedProteinSequenceBean> ReadWholeSequence(String queryProtein) {
final long startTime = System.currentTimeMillis();
String com = "SELECT JobID, Predictions FROM ProteinRow WHERE Protein = '" + queryProtein + "';";
System.out.println("Command: " + com);
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>();
+ List<AnnotatedProteinSequenceBean> res = new ArrayList<AnnotatedProteinSequenceBean>();
int c = 0;
for (Row r : rows) {
- StructureProteinPrediction structure = new StructureProteinPrediction(queryProtein, r.getString("JobID"), r.getMap(
+ AnnotatedProteinSequenceBean structure = new AnnotatedProteinSequenceBean(queryProtein, r.getString("JobID"), r.getMap(
"Predictions", String.class, String.class));
+ if (structure.getPrediction().containsKey("jnetpred"))
+ structure.setJnetpred(structure.getPrediction().get("jnetpred"));
+ else
+ structure.setJnetpred("");
res.add(structure);
++c;
}
/*
* getting part of protein sequence from the db ProteinRow
*/
- public List<StructureProteinPrediction> ReadPartOfSequence(String queryProtein) {
+ public List<AnnotatedProteinSequenceBean> ReadPartOfSequence(String queryProtein) {
final long startTime = System.currentTimeMillis();
String com = "SELECT * FROM ProteinRow;";
System.out.println("Command: " + com);
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>();
+ List<AnnotatedProteinSequenceBean> res = new ArrayList<AnnotatedProteinSequenceBean>();
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",
+ AnnotatedProteinSequenceBean structure = new AnnotatedProteinSequenceBean(prot, r.getString("JobID"), r.getMap("Predictions",
String.class, String.class));
res.add(structure);
++c;
}
/*
- * getting protein sequences by counter
+ * getting log info for jobid
*/
public StructureJobLog ReadJobLog(String jobid) {
final long startTime = System.currentTimeMillis();
import java.util.List;
import java.util.Map;
+import compbio.cassandra.AnnotatedProteinSequenceBean;
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;
+ private final static SimpleDateFormat formatYYMMDD = new SimpleDateFormat("yyyy/MM/dd");
+ private final static SimpleDateFormat formatDDMMYY = new SimpleDateFormat("dd/MM/yyyy");
/*
* query: execution time for the period from date1 till date2
if (null == date2) {
date1 = "2100/1/1";
}
- if (!isThisDateValid(date1) || !isThisDateValid(date2)) {
+ if (!isThisDateValid(date1,formatYYMMDD) || !isThisDateValid(date2,formatYYMMDD)) {
System.out.println("Wrong date: point 3");
return null;
}
SetDateRange();
int nbins = 5;
- long dateStart = DateParsing(date1);
- long dateEnd = DateParsing(date2);
+ long dateStart = DateParsing(date1, formatYYMMDD);
+ long dateEnd = DateParsing(date2, formatYYMMDD);
if (dateEnd < earlestDate || dateStart > currentDate || dateStart > dateEnd)
return null;
if (dateStart < earlestDate)
if (null == date2) {
date1 = "2100/1/1";
}
- if (!isThisDateValid(date1) || !isThisDateValid(date2)) {
+ if (!isThisDateValid(date1, formatYYMMDD) || !isThisDateValid(date2, formatYYMMDD)) {
System.out.println("Wrong date: point 3");
return null;
}
SetDateRange();
- long dateStart = DateParsing(date1);
- long dateEnd = DateParsing(date2);
+ long dateStart = DateParsing(date1, formatYYMMDD);
+ long dateEnd = DateParsing(date2, formatYYMMDD);
if (dateEnd < earlestDate || dateStart > currentDate || dateStart > dateEnd)
return null;
if (dateStart < earlestDate)
System.out.println("StatisticsProt.readLength: total number of dates = " + query.size());
return query;
}
-
- /*
- * query: jobs and sequence at date
- */
- public List<DataBase> readJobByDay (String date) {
- System.out.println(date);
- if (null == date) {
- return null;
- }
- if (!isThisDateValid(date, formatDDMMYY)) {
- System.out.println("Wrong date: point 3");
- return null;
- }
- SetDateRange();
- long day = DateParsing(date, formatDDMMYY);
- System.out.println(day);
- if (day < earlestDate || day > currentDate)
- return null;
- List<Pair<String, String>> res = db.ReadProteinData(day);
- if (res == null)
- return null;
- query = new ArrayList<DataBase>();
- for (Pair<String, String> entry : res) {
- DataBase bean = new DataBase();
- bean.setDate(date);
- bean.setId(entry.getElement0());
- bean.setProt(entry.getElement1());
- query.add(bean);
- }
- System.out.println("StatisticsProt.readLength: total number of dates = " + query.size());
- return query;
- }
+
/*
* query: protein sequence
* */
public List<DataBase> readProteins(String protIn, String flag) {
+ if (protIn == null)
+ return null;
+ System.out.println(protIn.length());
query = new ArrayList<DataBase>();
- List<StructureProteinPrediction> res;
+ List<AnnotatedProteinSequenceBean> res;
if (flag.equals("whole"))
res = db.ReadWholeSequence(protIn);
else
- res = db.ReadPartOfSequence(protIn);
+ res = (protIn.length() > 0) ? db.ReadPartOfSequence(protIn) : null;
if (res == null)
return null;
- for (StructureProteinPrediction entry : res) {
- DataBase bean = new DataBase();
- bean.setProt(entry.getSequence());
- bean.setId(entry.getJobid());
- bean.setJpred(entry.getJnetpred());
- if (flag.equals("part"))
- bean.setSubProt(CreateSubprot (entry.getSequence(), protIn));
- query.add(bean);
-
+ for (AnnotatedProteinSequenceBean entry : res) {
+ DataBase db = new DataBase();
+ db.setProt(entry.getSequence());
+ db.setPredictions(entry);
+ db.setId(entry.getJobid());
+ if (flag.equals("part")) {
+ db.setSubProt(CreateSubprot (entry.getSequence(), protIn));
+ }
+ query.add(db);
}
return query;
}
-
+
/*
* query protein sequences with number of jobs
*/
* query jobs log info
*/
public DataBase readJobLog(String jobid) {
- // query = new ArrayList<DataBase>();
+ if (jobid == null)
+ return null;
StructureJobLog res = db.ReadJobLog(jobid);
+ if (res == null)
+ return null;
DataBase query = new DataBase();
query.setLogInfo(res);
- // query.setres);
return query;
}
+
/*
* create list of parts of protein sequence;
*/
/*
* convert String date into long date (miliseconds since the epoch start)
*/
- private static long DateParsing(String datInput) {
+ private static long DateParsing(String datInput, SimpleDateFormat formatter) {
if (datInput == null) {
return 0;
}
long dateWorkSt = 0;
- SimpleDateFormat formatter = new SimpleDateFormat("yyyy/MM/dd");
+
try {
dateWorkSt = formatter.parse(datInput).getTime();
} catch (ParseException e) {
*/
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));
+ currentDate = DateParsing(cal.get(Calendar.YEAR) + "/" + (cal.get(Calendar.MONTH) + 1) + "/" + cal.get(Calendar.DAY_OF_MONTH), formatYYMMDD);
if (0 == earlestDate) {
CassandraRequester cr = new CassandraRequester();
earlestDate = cr.earliestDate();
}
}
- public boolean isThisDateValid(String dateToValidate) {
+ public boolean isThisDateValid(String dateToValidate, SimpleDateFormat sdf) {
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);
git://source.jalview.org / proteocache.git / commitdiff