.<String, PointSet>make().put("pointset", pset);
protected NavigableMap makeMap(KeyFunction keyfunc) { if (db == null) init(); String name = keyfunc.getClass().getName(); if (!db.exists(name)) return db.createTreeMap(name) .valueSerializer(new BlockSerializer()) .make(); else return db.getTreeMap(name); }
public static <K extends Comparable<K>, V> BTreeMap<K, V> batchCreate(final Map<K, V> map, BTreeMapMaker maker) { List<K> keys = Ordering.natural().reverse().sortedCopy(map.keySet()); return maker.pumpSource(keys.iterator(), new Fun.Function1<V, K>() { @Override public V run(K a) { return map.get(a); } }).make(); };
private void initTaxonCache() throws PropertyEnricherException { DB db = initDb("taxonCache"); String taxonCacheName = "taxonCacheById"; if (db.exists(taxonCacheName)) { resolvedIdToTaxonMap = db.getTreeMap(taxonCacheName); } else { LOG.info("local taxon cache of [" + taxonCache.getResource() + "] building..."); StopWatch watch = new StopWatch(); watch.start(); try { resolvedIdToTaxonMap = db .createTreeMap(taxonCacheName) .pumpPresort(100000) .pumpIgnoreDuplicates() .pumpSource(taxonCacheIterator(taxonCache)) .keySerializer(BTreeKeySerializer.STRING) .make(); } catch (IOException e) { throw new PropertyEnricherException("failed to instantiate taxonCache: [" + e.getMessage() + "]", e); } watch.stop(); logCacheLoadStats(watch.getTime(), resolvedIdToTaxonMap.size()); LOG.info("local taxon cache of [" + taxonCache.getResource() + "] built."); watch.reset(); } }
public static void exportDistinctInteractionsByStudy(ExportUtil.Appender writer, GraphDatabaseService graphDatabase, RowWriter rowWriter) throws IOException { DB db = DBMaker .newMemoryDirectDB() .compressionEnable() .transactionDisable() .make(); final Map<Fun.Tuple3<Long, String, String>, List<String>> studyOccAggregate = db.createTreeMap("studyOccAggregate").make(); NodeUtil.findStudies(graphDatabase, new StudyNodeListener() { @Override public void onStudy(StudyNode aStudy) { collectDistinctInteractions(aStudy, studyOccAggregate); } }); for (Map.Entry<Fun.Tuple3<Long, String, String>, List<String>> distinctInteractions : studyOccAggregate.entrySet()) { rowWriter.writeRow( writer, new StudyNode(graphDatabase.getNodeById(distinctInteractions.getKey().a)), distinctInteractions.getKey().b, distinctInteractions.getKey().c, distinctInteractions.getValue() ); } db.close(); }
public void indexInteractions() { DB db = DBMaker .newMemoryDirectDB() .compressionEnable() .transactionDisable() .make(); final Map<Fun.Tuple3<Long, String, Long>, Long> taxonInteractions = db .createTreeMap("ottIdMap") .make(); collectTaxonInteractions(taxonInteractions); createTaxonInteractions(taxonInteractions); db.close(); }
public static <K extends Comparable<K>, V> BTreeMap<K, V> batchCreate(final Entries<K, V> entries, BTreeMapMaker maker) { return maker.pumpSource(entries.batchInsertIterator()).make(); };
public static <K extends Comparable<K>, V> BTreeMap<K, V> batchCreate(final NavigableMap<K, V> map, BTreeMapMaker maker) { if(map.keySet().iterator().next() instanceof String) throw new IllegalArgumentException("Unicode String comparator is inconsistent."); return maker.pumpSource(Iterators.transform( map.descendingMap().entrySet().iterator(), new Function<Entry<K,V>,Tuple2<K,V>>(){ public Tuple2<K,V> apply(Entry<K,V> e){ return new Tuple2<K,V>(e.getKey(), e.getValue()); } })).make(); };
@Override public SortingBuffer<K, V> make() { Comparator<UniqueKey<K>> comparator = this.keyComparator != null ? new UniqueKeyComparator<K>(keyComparator) : new ComparableUniqueKeyComparator<K>(); BTreeKeySerializer<UniqueKey<K>> uniqueKeySerializer = new UniqueKeyBTreeSerializer<K>(keySerializer, comparator); BTreeMapMaker maker = db(useHeap).createTreeMap(name).keySerializer(uniqueKeySerializer) .valueSerializer(valueSerializer); if (keepsize) maker = maker.counterEnable(); NavigableMap<UniqueKey<K>, V> buffer = maker.make(); return new CloseableSortingBufferWithDuplicates<K, V>(name, useHeap, buffer); } }
@Override public SortingBuffer<K, V> make() { Comparator<UniqueKey<K>> comparator = this.keyComparator != null ? new UniqueKeyComparator<K>(keyComparator) : new ComparableUniqueKeyComparator<K>(); BTreeKeySerializer<UniqueKey<K>> uniqueKeySerializer = new UniqueKeyBTreeSerializer<K>(keySerializer, comparator); BTreeMapMaker maker = db(useHeap).createTreeMap(name).keySerializer(uniqueKeySerializer) .valueSerializer(valueSerializer); if (keepsize) maker = maker.counterEnable(); NavigableMap<UniqueKey<K>, V> buffer = maker.make(); return new CloseableSortingBufferWithDuplicates<K, V>(name, useHeap, buffer); } }
/** * Constructs Sorter with optional limit and optional distinct filtering * @param limit long limit, where Long.MAXLONG means no limit * @param distinct optional boolean switch to do not preserve multiple equal elements */ public Sorter(long limit, boolean distinct) { this.db = DBMaker.newTempFileDB().deleteFilesAfterClose().closeOnJvmShutdown().transactionDisable().make(); this.map = db.createTreeMap(MAP_NAME).make(); this.limit = limit; this.distinct = distinct; }
public static <K extends Comparable<K>, V> BTreeMap<K, V> batchCreate(final Map<K, V> map, BTreeMapMaker maker) { List<K> keys = Ordering.natural().reverse().sortedCopy(map.keySet()); return maker.pumpSource(keys.iterator(), new Fun.Function1<V, K>() { @Override public V run(K a) { return map.get(a); } }).make(); };
public static <K extends Comparable<K>, V> BTreeMap<K, V> batchCreate(final NavigableMap<K, V> map, BTreeMapMaker maker) { if(map.keySet().iterator().next() instanceof String) throw new IllegalArgumentException("Unicode String comparator is inconsistent."); return maker.pumpSource(Iterators.transform( map.descendingMap().entrySet().iterator(), new Function<Entry<K,V>,Tuple2<K,V>>(){ public Tuple2<K,V> apply(Entry<K,V> e){ return new Tuple2<K,V>(e.getKey(), e.getValue()); } })).make(); };
protected NavigableMap makeMap(KeyFunction keyfunc) { if (db == null) init(); String name = keyfunc.getClass().getName(); if (!db.exists(name)) return db.createTreeMap(name) .valueSerializer(new BlockSerializer()) .make(); else return db.getTreeMap(name); }
public static <K extends Comparable<K>, V> BTreeMap<K, V> batchCreate(final NavigableMap<K, V> map, BTreeMapMaker maker) { if(map.keySet().iterator().next() instanceof String) throw new IllegalArgumentException("Unicode String comparator is inconsistent."); return maker.pumpSource(Iterators.transform( map.descendingMap().entrySet().iterator(), new Function<Entry<K,V>,Tuple2<K,V>>(){ public Tuple2<K,V> apply(Entry<K,V> e){ return new Tuple2<K,V>(e.getKey(), e.getValue()); } })).make(); };
public static <K extends Comparable<K>, V> BTreeMap<K, V> batchCreate(final Entries<K, V> entries, BTreeMapMaker maker) { return maker.pumpSource(entries.batchInsertIterator()).make(); };
public static <K extends Comparable<K>, V> BTreeMap<K, V> batchCreate(final Entries<K, V> entries, BTreeMapMaker maker) { return maker.pumpSource(entries.batchInsertIterator()).make(); };
@Override public SortingBuffer<K, V> make() { BTreeMapMaker maker = db(useHeap).createTreeMap(name).keySerializer(keySerializer).valueSerializer(valueSerializer); if (keepsize) maker = maker.counterEnable(); NavigableMap<K, V> buffer = maker.make(); return new CloseableSortingBuffer<K, V>(name, useHeap, buffer); } }
@Override public SortingBuffer<K, V> make() { BTreeMapMaker maker = db(useHeap).createTreeMap(name).keySerializer(keySerializer).valueSerializer(valueSerializer); if (keepsize) maker = maker.counterEnable(); NavigableMap<K, V> buffer = maker.make(); return new CloseableSortingBuffer<K, V>(name, useHeap, buffer); } }
public static <K extends Comparable<K>, V> BTreeMap<K, V> batchCreate(final Map<K, V> map, BTreeMapMaker maker) { List<K> keys = Ordering.natural().reverse().sortedCopy(map.keySet()); return maker.pumpSource(keys.iterator(), new Fun.Function1<V, K>() { @Override public V run(K a) { return map.get(a); } }).make(); };