void add(long key, Index index) {
if (stdOut.start < 0) {
stdOut.start = index.stdOut.start;
}
if (stdErr.start < 0) {
stdErr.start = index.stdErr.start;
}
if (index.stdOut.stop > stdOut.stop) {
stdOut.stop = index.stdOut.stop;
}
if (index.stdErr.stop > stdErr.stop) {
stdErr.stop = index.stdErr.stop;
}
children.put(key, index);
}
private void mark(long classId, long testId, boolean isStdout) {
if (!index.containsKey(classId)) {
index.put(classId, new LinkedHashMap<Long, TestCaseRegion>());
}
Map<Long, TestCaseRegion> testCaseRegions = index.get(classId);
if (!testCaseRegions.containsKey(testId)) {
TestCaseRegion region = new TestCaseRegion();
testCaseRegions.put(testId, region);
}
TestCaseRegion region = testCaseRegions.get(testId);
Region streamRegion = isStdout ? region.stdOutRegion : region.stdErrRegion;
int total = output.total();
if (streamRegion.start < 0) {
streamRegion.start = total;
}
streamRegion.stop = total;
}
private Pair<Region, Region> findProbePair(
String primerName, Map<String, Set<Region>> primerHits) {
String leftName = String.format("%s_left", primerName);
String rightName = String.format("%s_right", primerName);
if (!primerHits.containsKey(leftName) || !primerHits.containsKey(rightName)) {
return null;
}
if (primerHits.get(leftName).size() != 1 || primerHits.get(rightName).size() != 1) {
return null;
}
Iterator<Region> leftitr = primerHits.get(leftName).iterator();
Iterator<Region> rightitr = primerHits.get(rightName).iterator();
Region left = leftitr.next();
Region right = rightitr.next();
if (!left.getChrom().equals(right.getChrom())) {
return null;
}
return new Pair<Region, Region>(left, right);
}
public Collection<NamedRegion> parseProbes() throws IOException {
double ethreshold = 1.0e-3;
Parser<BlastTabEntry> parser =
new Parser<BlastTabEntry>(blasttab, new BlastTabEntry.ParsingMapper());
Iterator<BlastTabEntry> itr =
new FilterIterator<BlastTabEntry, BlastTabEntry>(
new BlastTabEntry.ExpectedScoreFilter(ethreshold), parser);
Map<String, Set<Region>> primerHits = new TreeMap<String, Set<Region>>();
Set<String> primerNames = new TreeSet<String>();
while (itr.hasNext()) {
BlastTabEntry entry = itr.next();
NamedRegion r = createNamedRegion(entry);
if (!primerHits.containsKey(entry.getQuery())) {
primerHits.put(entry.getQuery(), new HashSet<Region>());
}
primerHits.get(entry.getQuery()).add(r);
primerNames.add(removePrimerLR(entry.getQuery()));
}
LinkedList<NamedRegion> probes = new LinkedList<NamedRegion>();
for (String primerName : primerNames) {
Pair<Region, Region> hits = findProbePair(primerName, primerHits);
if (hits != null) {
Region left = hits.getFirst(), right = hits.getLast();
int start = Math.min(left.getStart(), right.getStart());
int end = Math.max(left.getEnd(), right.getEnd());
NamedRegion probe = new NamedRegion(genome, left.getChrom(), start, end, primerName);
probes.addLast(probe);
}
}
return probes;
}
private void saveExcelPoject(File file) throws IOException {
Workbook wb = new XSSFWorkbook();
Sheet sheet = wb.createSheet("timeplan");
// Заголовок в 0 строке
Row row = sheet.createRow(0);
Cell cell = row.createCell(0);
cell.setCellValue("Филиал");
cell = row.createCell(1);
cell.setCellValue("Город");
Calendar cal = Calendar.getInstance();
cal.set(2017, 0, 5); // Начальная дата проекта
SimpleDateFormat sdf = new SimpleDateFormat("dd.MM.yy");
for (int i = 0; i < 3 * 52; i++) { // Счетчик по неделям
cell = row.createCell(i + 2);
cell.setCellValue(sdf.format(cal.getTime()));
cal.add(Calendar.WEEK_OF_YEAR, 1); // Следующая неделя
}
// sheet.setColumnWidth(0, 256);
// Цвета ячеек
CellStyle[] styles = new CellStyle[6];
styles[0] = wb.createCellStyle();
styles[0].setFillForegroundColor(HSSFColor.RED.index);
styles[0].setFillPattern(FillPatternType.SOLID_FOREGROUND);
styles[1] = wb.createCellStyle();
styles[1].setFillForegroundColor(HSSFColor.GREEN.index);
styles[1].setFillPattern(FillPatternType.SOLID_FOREGROUND);
styles[2] = wb.createCellStyle();
styles[2].setFillForegroundColor(HSSFColor.BLUE.index);
styles[2].setFillPattern(FillPatternType.SOLID_FOREGROUND);
styles[3] = wb.createCellStyle();
styles[3].setFillForegroundColor(HSSFColor.ROSE.index);
styles[3].setFillPattern(FillPatternType.SOLID_FOREGROUND);
styles[4] = wb.createCellStyle();
styles[4].setFillForegroundColor(HSSFColor.LIGHT_BLUE.index);
styles[4].setFillPattern(FillPatternType.SOLID_FOREGROUND);
styles[5] = wb.createCellStyle();
styles[5].setFillForegroundColor(HSSFColor.LIGHT_GREEN.index);
styles[5].setFillPattern(FillPatternType.SOLID_FOREGROUND);
short rowIdx = 0;
for (Region region : this.regions) {
row = sheet.createRow(++rowIdx);
cell = row.createCell(0);
cell.setCellValue(region.filial);
cell = row.createCell(1);
cell.setCellValue(region.name);
cal = Calendar.getInstance();
cal.set(2017, 0, 5); // Начальная дата проекта
for (int i = 0; i < 3 * 52; i++) { // Счетчик по неделям
short color = region.getDateColorIndex(cal.getTime());
if (color >= 0) {
cell = row.createCell(i + 2);
cell.setCellStyle(styles[color]);
}
cal.add(Calendar.WEEK_OF_YEAR, 1); // Следующая неделя
}
}
try (FileOutputStream fileOut = new FileOutputStream(file)) {
wb.write(fileOut);
}
}
RTreeLoad(String[] args) {
try {
if (args.length != 4) {
System.err.println(
"Usage: RTreeLoad input_file tree_file capacity query_type [intersection | 10NN].");
System.exit(-1);
}
LineNumberReader lr = null;
try {
lr = new LineNumberReader(new FileReader(args[0]));
} catch (FileNotFoundException e) {
System.err.println("Cannot open data file " + args[0] + ".");
System.exit(-1);
}
// Create a disk based storage manager.
PropertySet ps = new PropertySet();
Boolean b = new Boolean(true);
ps.setProperty("Overwrite", b);
// overwrite the file if it exists.
ps.setProperty("FileName", args[1]);
// .idx and .dat extensions will be added.
Integer i = new Integer(4096);
ps.setProperty("PageSize", i);
// specify the page size. Since the index may also contain user defined data
// there is no way to know how big a single node may become. The storage manager
// will use multiple pages per node if needed. Off course this will slow down performance.
IStorageManager diskfile = new DiskStorageManager(ps);
IBuffer file = new RandomEvictionsBuffer(diskfile, 10, false);
// applies a main memory random buffer on top of the persistent storage manager
// (LRU buffer, etc can be created the same way).
// Create a new, empty, RTree with dimensionality 2, minimum load 70%, using "file" as
// the StorageManager and the RSTAR splitting policy.
PropertySet ps2 = new PropertySet();
Double f = new Double(0.7);
ps2.setProperty("FillFactor", f);
i = new Integer(args[2]);
ps2.setProperty("IndexCapacity", i);
ps2.setProperty("LeafCapacity", i);
// Index capacity and leaf capacity may be different.
i = new Integer(2);
ps2.setProperty("Dimension", i);
ISpatialIndex tree = new RTree(ps2, file);
int count = 0;
int indexIO = 0;
int leafIO = 0;
int id, op;
double x1, x2, y1, y2;
double[] f1 = new double[2];
double[] f2 = new double[2];
long start = System.currentTimeMillis();
String line = lr.readLine();
while (line != null) {
StringTokenizer st = new StringTokenizer(line);
op = new Integer(st.nextToken()).intValue();
id = new Integer(st.nextToken()).intValue();
x1 = new Double(st.nextToken()).doubleValue();
y1 = new Double(st.nextToken()).doubleValue();
x2 = new Double(st.nextToken()).doubleValue();
y2 = new Double(st.nextToken()).doubleValue();
if (op == 0) {
// delete
f1[0] = x1;
f1[1] = y1;
f2[0] = x2;
f2[1] = y2;
Region r = new Region(f1, f2);
if (tree.deleteData(r, id) == false) {
System.err.println("Cannot delete id: " + id + " , count: " + count + ".");
System.exit(-1);
}
} else if (op == 1) {
// insert
f1[0] = x1;
f1[1] = y1;
f2[0] = x2;
f2[1] = y2;
Region r = new Region(f1, f2);
String data = r.toString();
// associate some data with this region. I will use a string that represents the
// region itself, as an example.
// NOTE: It is not necessary to associate any data here. A null pointer can be used. In
// that
// case you should store the data externally. The index will provide the data IDs of
// the answers to any query, which can be used to access the actual data from the external
// storage (e.g. a hash table or a database table, etc.).
// Storing the data in the index is convinient and in case a clustered storage manager is
// provided (one that stores any node in consecutive pages) performance will improve
// substantially,
// since disk accesses will be mostly sequential. On the other hand, the index will need
// to
// manipulate the data, resulting in larger overhead. If you use a main memory storage
// manager,
// storing the data externally is highly recommended (clustering has no effect).
// A clustered storage manager is NOT provided yet.
// Also you will have to take care of converting you data to and from binary format, since
// only
// array of bytes can be inserted in the index (see RTree::Node::load and
// RTree::Node::store for
// an example of how to do that).
// tree.insertData(data.getBytes(), r, id);
tree.insertData(null, r, id);
// example of passing a null pointer as the associated data.
} else if (op == 2) {
// query
f1[0] = x1;
f1[1] = y1;
f2[0] = x2;
f2[1] = y2;
MyVisitor vis = new MyVisitor();
if (args[3].equals("intersection")) {
Region r = new Region(f1, f2);
tree.intersectionQuery(r, vis);
// this will find all data that intersect with the query range.
} else if (args[3].equals("10NN")) {
Point p = new Point(f1);
tree.nearestNeighborQuery(10, p, vis);
// this will find the 10 nearest neighbors.
} else {
System.err.println("Unknown query type.");
System.exit(-1);
}
}
if ((count % 1000) == 0) System.err.println(count);
count++;
line = lr.readLine();
}
long end = System.currentTimeMillis();
System.err.println("Operations: " + count);
System.err.println(tree);
System.err.println("Minutes: " + ((end - start) / 1000.0f) / 60.0f);
// since we created a new RTree, the PropertySet that was used to initialize the structure
// now contains the IndexIdentifier property, which can be used later to reuse the index.
// (Remember that multiple indices may reside in the same storage manager at the same time
// and every one is accessed using its unique IndexIdentifier).
Integer indexID = (Integer) ps2.getProperty("IndexIdentifier");
System.err.println("Index ID: " + indexID);
boolean ret = tree.isIndexValid();
if (ret == false) System.err.println("Structure is INVALID!");
// flush all pending changes to persistent storage (needed since Java might not call finalize
// when JVM exits).
tree.flush();
} catch (Exception e) {
e.printStackTrace();
}
}
