From: Sasha Sherstnev <a.sherstnev@dundee.ac.uk>
Date: Mon, 28 Oct 2013 20:20:16 +0000 (+0000)
Subject: Optimize code
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=5058bbff61abfcc34d734124545f86b2029b3373;p=proteocache.git

Optimize code
---

diff --git a/server/compbio/statistic/StatisticsProt.java b/server/compbio/statistic/StatisticsProt.java
index 02e7a59..0294747 100644
--- a/server/compbio/statistic/StatisticsProt.java
+++ b/server/compbio/statistic/StatisticsProt.java
@@ -26,111 +26,122 @@ public class StatisticsProt {
 	private final static long MILLISECONDS_PER_DAY = 1000L * 60 * 60 * 24;
 	private CassandraCreate cc = new CassandraCreate();
 	private ArrayList<DataBase> query;
+	private static long currentDate = 0;
+	private static long earlestDate = 0;
 
-	// query for the period from date1 till date2
-	public List<DataBase> readDetail(String dateInStringSt, String dateInStringEnd) {
-		if (!isThisDateValid(dateInStringSt))
+	/* query: the period from date1 till date2 */
+	public List<DataBase> readDetails(String date1, String date2) {
+		if (!isThisDateValid(date1) || !isThisDateValid(date2)) {
+			System.out.println("Wrong date: point 1");
 			return null;
-		long dateWorkSt = DateParsing(dateInStringSt);
-		long dateWorkEnd = DateParsing(dateInStringEnd);
-		if (CheckDate(dateWorkSt) && CheckDate(dateWorkEnd)) {
-			query = new ArrayList<DataBase>();
-			while (dateWorkSt <= dateWorkEnd) {
-				SliceQuery<Long, String, String> result = HFactory.createSliceQuery(cc.GetKeyspace(), LongSerializer.get(),
-						StringSerializer.get(), StringSerializer.get());
-				result.setColumnFamily("ProteinData");
-				result.setKey(dateWorkSt);
-				result.setRange(null, null, false, Integer.MAX_VALUE);
-				QueryResult<ColumnSlice<String, String>> columnSlice = result.execute();
-				if (!columnSlice.get().getColumns().isEmpty()) {
-					DataBase db = new DataBase(DateFormat(dateWorkSt), columnSlice.get().getColumns().size());
-					query.add(db);
-				}
-				dateWorkSt += MILLISECONDS_PER_DAY;
+		}
+		SetDateRange();
+
+		long dateStart = DateParsing(date1);
+		long dateEnd = DateParsing(date2);
+		if (dateStart < earlestDate)
+			dateStart = earlestDate;
+		if (dateStart > currentDate)
+			dateStart = currentDate - MILLISECONDS_PER_DAY;
+		if (dateEnd < earlestDate)
+			dateStart = earlestDate + MILLISECONDS_PER_DAY;
+		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);
+
+		query = new ArrayList<DataBase>();
+		int day = 0;
+		while (dateStart <= dateEnd) {
+			SliceQuery<Long, String, String> result = HFactory.createSliceQuery(cc.GetKeyspace(), LongSerializer.get(),
+					StringSerializer.get(), StringSerializer.get());
+			result.setColumnFamily("ProteinData");
+			result.setKey(dateStart);
+			result.setRange(null, null, false, Integer.MAX_VALUE);
+			QueryResult<ColumnSlice<String, String>> columnSlice = result.execute();
+			++day;
+			System.out.print("Day " + day + ": dataStart = " + dateStart + ": ");
+			if (!columnSlice.get().getColumns().isEmpty()) {
+				DataBase db = new DataBase(DateFormat(dateStart), columnSlice.get().getColumns().size());
+				query.add(db);
+				System.out.println("data exist");
+			} else {
+				System.out.println("no data");
 			}
-		} else
-			System.out.println("Wrong date");
+			dateStart += MILLISECONDS_PER_DAY;
+		}
+		System.out.println("StatisticsProt.readLength: total number of dates = " + query.size());
 		return query;
 	}
 
-	// find the earliest date
-	public long earliestDate() {
-		ArrayList<Long> dateSort = new ArrayList<Long>();
-		int row_count = 10000;
-		RangeSlicesQuery<Long, String, String> 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<OrderedRows<Long, String, String>> columnSlice = result.execute();
-			OrderedRows<Long, String, String> rows = columnSlice.get();
-			Iterator<Row<Long, String, String>> rowsIterator = rows.iterator();
-			while (rowsIterator.hasNext()) {
-				Row<Long, String, String> row = rowsIterator.next();
-				last_key = row.getKey();
-				dateSort.add(last_key);
-			}
-			if (rows.getCount() < row_count)
-				break;
+	/*
+	 * query: execution time for the period from date1 till date2
+	 */
+	public List<DataBase> readLength(String date1, String date2) {
+		if (!isThisDateValid(date1) || !isThisDateValid(date2)) {
+			System.out.println("Wrong date: point 3");
+			return null;
 		}
-		Collections.sort(dateSort);
-		return dateSort.get(0);
-	}
+		SetDateRange();
 
-	// query execution time for the period from dateInStringSt till
-	// dateInStringEnd
-	public List<DataBase> readLength(String dateInStringSt, String dateInStringEnd) {
-		long dateWorkSt = DateParsing(dateInStringSt);
-		long dateWorkEnd = DateParsing(dateInStringEnd);
-		if (CheckDate(dateWorkSt) && CheckDate(dateWorkEnd)) {
-			query = new ArrayList<DataBase>();
-			List<Integer> totalTime = new ArrayList<Integer>();
-			for (int i = 0; i < 4; i++)
-				totalTime.add(i, 0);
-			while (dateWorkSt <= dateWorkEnd) {
-				List<Integer> timeResult = new ArrayList<Integer>();
-				SliceQuery<Long, String, String> result = HFactory.createSliceQuery(cc.GetKeyspace(), LongSerializer.get(),
-						StringSerializer.get(), StringSerializer.get());
-				result.setColumnFamily("ProteinData");
-				result.setKey(dateWorkSt);
-				result.setRange(null, null, false, Integer.MAX_VALUE);
-				QueryResult<ColumnSlice<String, String>> columnSlice = result.execute();
-				List<HColumn<String, String>> col = columnSlice.get().getColumns();
-				if (!col.isEmpty()) {
-					Iterator<HColumn<String, String>> itCol = col.iterator();
-					for (int i = 0; i < 4; i++)
-						timeResult.add(i, 0);
-					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 {
-							timeResult.set(3, timeResult.get(3) + 1);
-							// System.out.println(lenResult + "; " + id);
-						}
+		long dateStart = DateParsing(date1);
+		long dateEnd = DateParsing(date2);
+		if (dateStart < earlestDate)
+			dateStart = earlestDate;
+		if (dateStart > currentDate)
+			dateStart = currentDate - MILLISECONDS_PER_DAY;
+		if (dateEnd < earlestDate)
+			dateStart = earlestDate + MILLISECONDS_PER_DAY;
+		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);
+
+		query = new ArrayList<DataBase>();
+		List<Integer> totalTime = new ArrayList<Integer>();
+		for (int i = 0; i < 4; i++)
+			totalTime.add(i, 0);
+		while (dateStart <= dateEnd) {
+			List<Integer> timeResult = new ArrayList<Integer>();
+			SliceQuery<Long, String, String> result = HFactory.createSliceQuery(cc.GetKeyspace(), LongSerializer.get(),
+					StringSerializer.get(), StringSerializer.get());
+			result.setColumnFamily("ProteinData");
+			result.setKey(dateStart);
+			result.setRange(null, null, false, Integer.MAX_VALUE);
+			QueryResult<ColumnSlice<String, String>> columnSlice = result.execute();
+			List<HColumn<String, String>> col = columnSlice.get().getColumns();
+			if (!col.isEmpty()) {
+				Iterator<HColumn<String, String>> itCol = col.iterator();
+				for (int i = 0; i < 4; i++)
+					timeResult.add(i, 0);
+				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 {
+						timeResult.set(3, timeResult.get(3) + 1);
 					}
-					DataBase db = new DataBase();
-					db.setTimeRez(timeResult);
-					db.setDate(DateFormat(dateWorkSt));
-					query.add(db);
 				}
-				dateWorkSt += MILLISECONDS_PER_DAY;
+				DataBase db = new DataBase();
+				db.setTimeRez(timeResult);
+				db.setDate(DateFormat(dateStart));
+				query.add(db);
 			}
-		} else
-			System.out.println("Wrong date");
+			dateStart += MILLISECONDS_PER_DAY;
+		}
+		System.out.println("StatisticsProt.readLength: total number of dates = " + query.size());
 		return query;
 	}
 
-	// query by a protein sequence
-	public List<DataBase> readProt(String protIn) {
+	/* query: protein sequence */
+	public List<DataBase> readProteins(String protIn) {
 		query = new ArrayList<DataBase>();
 		SliceQuery<String, String, String> result = HFactory.createSliceQuery(cc.GetKeyspace(), StringSerializer.get(),
 				StringSerializer.get(), StringSerializer.get());
@@ -141,11 +152,14 @@ public class StatisticsProt {
 		Iterator<HColumn<String, String>> it = columnSlice.get().getColumns().iterator();
 		while (it.hasNext()) {
 			HColumn<String, String> col = it.next();
-			DataBase db = new DataBase();
-			db.setProt(protIn);
-			db.setId(col.getName());
-			db.setJpred(col.getValue());
-			query.add(db);
+			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;
 	}
@@ -168,10 +182,18 @@ public class StatisticsProt {
 			while (rowsIterator.hasNext()) {
 				Row<String, String, String> row = rowsIterator.next();
 				last_key = row.getKey();
-				if (row.getColumnSlice().getColumns().size() > 3) {
+				List<HColumn<String, String>> clms = row.getColumnSlice().getColumns();
+				int npred = 0;
+				for (HColumn<String, String> cln : clms) {
+					String name = cln.getName();
+					if (name.matches("(.*)jnetpred")) {
+						++npred;
+					}
+				}
+				if (npred > 3) {
 					DataBase db = new DataBase();
 					db.setProt(last_key);
-					db.setTotalId(row.getColumnSlice().getColumns().size());
+					db.setTotalId(npred);
 					query.add(db);
 				}
 			}
@@ -214,12 +236,15 @@ public class StatisticsProt {
 						}
 						if (subStr.length() > 0)
 							subProt.add(subStr);
-						DataBase db = new DataBase();
-						db.setProt(last_key);
-						db.setId(col.getName());
-						db.setJpred(col.getValue());
-						db.setSubProt(subProt);
-						query.add(db);
+						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);
+						}
 					}
 				}
 			}
@@ -256,8 +281,6 @@ public class StatisticsProt {
 		} catch (ParseException e) {
 			e.printStackTrace();
 		}
-		// System.out.println(datInput + "start reverce" +
-		// DateFormat1(dateWorkSt));
 		return dateWorkSt;
 	}
 
@@ -268,12 +291,11 @@ public class StatisticsProt {
 		return dateString;
 	}
 
-	private static String DateFormat1(long inDate) {
-		SimpleDateFormat datformat = new SimpleDateFormat("yyyy/MM/dd:hh:mm:ss");
-		String dateString = datformat.format(new Date(inDate));
-		return dateString;
-	}
-
+	/*
+	 * private static String DateFormat1(long inDate) { SimpleDateFormat
+	 * datformat = new SimpleDateFormat("yyyy/MM/dd:hh:mm:ss"); String
+	 * dateString = datformat.format(new Date(inDate)); return dateString; }
+	 */
 	public static String DateFormatYYMMDD(long indate) {
 		SimpleDateFormat datformat = new SimpleDateFormat("yyyy/MM/dd");
 		String dateString = datformat.format(new Date(indate));
@@ -291,32 +313,28 @@ public class StatisticsProt {
 		long datBeginLong = TimeConvert(datBegin);
 		long datEndLong = TimeConvert(datEnd);
 		return (datEndLong - datBeginLong) / 1000;
-
 	}
 
-	public static boolean CheckDate(long indate) {
-		if (indate == 0) {
-			return false;
+	private static void SetDateRange() {
+		if (0 == earlestDate) {
+			StatisticsProt sp = new StatisticsProt();
+			earlestDate = sp.earliestDate();
+			System.out.println("Set earlest Date = " + earlestDate);
 		}
-		StatisticsProt sp = new StatisticsProt();
 		Calendar cal = Calendar.getInstance();
-		String currentDate = cal.get(Calendar.YEAR) + "/" + (cal.get(Calendar.MONTH) + 1) + "/" + cal.get(Calendar.DAY_OF_MONTH);
-		if (indate >= sp.earliestDate() && indate <= DateParsing(currentDate)) {
-			return true;
-		}
-		return false;
+		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) {
+		if (dateToValidate == null || dateToValidate.equals("")) {
+			System.out.println("Undefined date");
 			return false;
 		}
 		SimpleDateFormat sdf = new SimpleDateFormat("yyyy/MM/dd");
 		try {
-			// if not valid, it will throw ParseException
+			// if not valid, this will throw ParseException
 			sdf.setLenient(false);
 			Date date = sdf.parse(dateToValidate);
-			// System.out.println(date);
 		} catch (ParseException e) {
 			e.printStackTrace();
 			return false;
@@ -324,4 +342,30 @@ public class StatisticsProt {
 		return true;
 	}
 
+	// find the earliest date
+	public long earliestDate() {
+		ArrayList<Long> dateSort = new ArrayList<Long>();
+		int row_count = 10000;
+		RangeSlicesQuery<Long, String, String> 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<OrderedRows<Long, String, String>> columnSlice = result.execute();
+			OrderedRows<Long, String, String> rows = columnSlice.get();
+			Iterator<Row<Long, String, String>> rowsIterator = rows.iterator();
+			while (rowsIterator.hasNext()) {
+				Row<Long, String, String> row = rowsIterator.next();
+				last_key = row.getKey();
+				dateSort.add(last_key);
+			}
+			if (rows.getCount() < row_count)
+				break;
+		}
+		Collections.sort(dateSort);
+		return dateSort.get(0);
+	}
 }