From d616db97e837bcde43c939f228993c7d6e396a3c Mon Sep 17 00:00:00 2001 From: Sasha Sherstnev Date: Thu, 19 Dec 2013 12:38:26 +0000 Subject: [PATCH] Remove obsolete classes --- server/compbio/listeners/DetailList.java | 45 --- server/compbio/statistic/StatisticsProt.java | 402 -------------------------- 2 files changed, 447 deletions(-) delete mode 100644 server/compbio/listeners/DetailList.java delete mode 100755 server/compbio/statistic/StatisticsProt.java diff --git a/server/compbio/listeners/DetailList.java b/server/compbio/listeners/DetailList.java deleted file mode 100644 index 035b770..0000000 --- a/server/compbio/listeners/DetailList.java +++ /dev/null @@ -1,45 +0,0 @@ -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.*; - -/** - * 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 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/server/compbio/statistic/StatisticsProt.java b/server/compbio/statistic/StatisticsProt.java deleted file mode 100755 index 05375c0..0000000 --- a/server/compbio/statistic/StatisticsProt.java +++ /dev/null @@ -1,402 +0,0 @@ -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 query; - private static long currentDate = 0; - private static long earlestDate = 0; - - /* - * query: the period from date1 till date2 - * */ - public List 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(); - int day = 0; - /* - for (Date date = start.getTime(); !start.after(end); start.add(Calendar.DATE, 1), date = start.getTime()) { - SliceQuery 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 = 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 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(); - List totalTime = new ArrayList(); - 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 timeResult = new ArrayList(); - SliceQuery 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 = result.execute(); - List> col = columnSlice.get().getColumns(); - if (!col.isEmpty()) { - Iterator> 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 readProteins(String protIn) { - query = new ArrayList(); - /* - SliceQuery 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 = result.execute(); - Iterator> it = columnSlice.get().getColumns().iterator(); - while (it.hasNext()) { - HColumn 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 readProtID(int counter) { - query = new ArrayList(); - int row_count = 100; - /* - RangeSlicesQuery 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> columnSlice = result.execute(); - OrderedRows rows = columnSlice.get(); - Iterator> rowsIterator = rows.iterator(); - while (rowsIterator.hasNext()) { - Row row = rowsIterator.next(); - last_key = row.getKey(); - List> clms = row.getColumnSlice().getColumns(); - //int npred = 0; - //for (HColumn 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 readPart(String protIn) { - int row_count = 10000; - query = new ArrayList(); - /* - RangeSlicesQuery 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> columnSlice = result.execute(); - OrderedRows rows = columnSlice.get(); - Iterator> rowsIterator = rows.iterator(); - while (rowsIterator.hasNext()) { - Row row = rowsIterator.next(); - last_key = row.getKey(); - if (last_key.matches("(.*)" + protIn + "(.*)")) { - Iterator> it = row.getColumnSlice().getColumns().iterator(); - while (it.hasNext()) { - HColumn col = it.next(); - List subProt = new ArrayList(); - 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 sliceQuery = HFactory.createSliceQuery(cc.GetKeyspace(), StringSerializer.get(), - StringSerializer.get(), StringSerializer.get()); - sliceQuery.setColumnFamily("ProteinLog").setKey(id).setRange("", "", false, 100); - QueryResult> 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 dateSort = new ArrayList(); - int row_count = 10000; - /* - RangeSlicesQuery 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> columnSlice = result.execute(); - OrderedRows rows = columnSlice.get(); - Iterator> rowsIterator = rows.iterator(); - while (rowsIterator.hasNext()) { - Row row = rowsIterator.next(); - last_key = row.getKey(); - dateSort.add(last_key); - } - if (rows.getCount() < row_count) - break; - }*/ - Collections.sort(dateSort); - return dateSort.get(0); - } -} -- 1.7.10.2