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());
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;
}
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);
}
}
}
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);
+ }
}
}
}
} catch (ParseException e) {
e.printStackTrace();
}
- // System.out.println(datInput + "start reverce" +
- // DateFormat1(dateWorkSt));
return dateWorkSt;
}
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));
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;
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);
+ }
}
git://source.jalview.org / proteocache.git / commitdiff