/** {@inheritDoc} */ @SuppressWarnings({"unchecked"}) public Object[] values() { Object[] vals = new Object[size()]; V[] v = _values; byte[] states = _states; for ( int i = v.length, j = 0; i-- > 0; ) { if ( states[i] == FULL ) { vals[j++] = v[i]; } } return vals; }
public int NZN() { return vector.size(); }
/** {@inheritDoc} */ @SuppressWarnings({"unchecked"}) public long[] keys() { long[] keys = new long[size()]; long[] k = _set; byte[] states = _states; for ( int i = k.length, j = 0; i-- > 0; ) { if ( states[i] == FULL ) { keys[j++] = k[i]; } } return keys; }
public void printDebugMemoryInformation(RoutingContext ctx, PriorityQueue<RouteSegment> graphDirectSegments, PriorityQueue<RouteSegment> graphReverseSegments, TLongObjectHashMap<RouteSegment> visitedDirectSegments,TLongObjectHashMap<RouteSegment> visitedOppositeSegments) { printInfo("Time to calculate : " + (System.nanoTime() - ctx.timeToCalculate) / 1e6 + ", time to load : " + ctx.timeToLoad / 1e6 + ", time to load headers : " + ctx.timeToLoadHeaders / 1e6 + ", time to calc dev : " + ctx.timeNanoToCalcDeviation/ 1e6); int maxLoadedTiles = Math.max(ctx.maxLoadedTiles, ctx.getCurrentlyLoadedTiles()); printInfo("Current loaded tiles : " + ctx.getCurrentlyLoadedTiles() + ", maximum loaded tiles " + maxLoadedTiles); printInfo("Loaded tiles " + ctx.loadedTiles + " (distinct " + ctx.distinctLoadedTiles + "), unloaded tiles " + ctx.unloadedTiles + ", loaded more than once same tiles " + ctx.loadedPrevUnloadedTiles); printInfo("Visited roads " + ctx.visitedSegments + ", relaxed roads " + ctx.relaxedSegments); if (graphDirectSegments != null && graphReverseSegments != null) { printInfo("Priority queues sizes : " + graphDirectSegments.size() + "/" + graphReverseSegments.size()); } if (visitedDirectSegments != null && visitedOppositeSegments != null) { printInfo("Visited interval sizes: " + visitedDirectSegments.size() + "/" + visitedOppositeSegments.size()); } }
System.out.println(String.format("Calculated %.1f seconds, found %d results, visited %d routes, loaded %d tiles (%d ms read, %d ms total),", (System.currentTimeMillis() - ctx.startCalcTime) / 1000.0, results.size(), ctx.visitedRoutesCount, ctx.quadTree.size(), ctx.readTime / (1000 * 1000), ctx.loadTime / (1000 * 1000))); for(TransportRouteSegment res : results) { if (ctx.calculationProgress != null && ctx.calculationProgress.isCancelled) {
/** {@inheritDoc} */ public boolean equals( Object other ) { if ( ! ( other instanceof TLongObjectMap ) ) { return false; } TLongObjectMap that = ( TLongObjectMap ) other; if ( that.size() != this.size() ) { return false; } try { TLongObjectIterator iter = this.iterator(); while ( iter.hasNext() ) { iter.advance(); long key = iter.key(); Object value = iter.value(); if ( value == null ) { if ( !( that.get( key ) == null && that.containsKey( key ) ) ) { return false; } } else { if ( !value.equals( that.get( key ) ) ) { return false; } } } } catch ( ClassCastException ex ) { // unused. } return true; }
/** * Get the number of reference frames that have already been registered. * @return int */ public int getNumberOfReferenceFramesRegistered() { return referenceFrames.size(); }
/** {@inheritDoc} */ @SuppressWarnings({"unchecked"}) public V[] values() { V[] vals = ( V[] ) new Object[size()]; V[] v = _values; byte[] states = _states; for ( int i = v.length, j = 0; i-- > 0; ) { if ( states[i] == FULL ) { vals[j++] = v[i]; } } return vals; }
/** {@inheritDoc} */ @SuppressWarnings({"unchecked"}) public long[] keys() { long[] keys = new long[size()]; long[] k = _set; byte[] states = _states; for ( int i = k.length, j = 0; i-- > 0; ) { if ( states[i] == FULL ) { keys[j++] = k[i]; } } return keys; }
/** {@inheritDoc} */ @SuppressWarnings({"unchecked"}) public Object[] values() { Object[] vals = new Object[size()]; V[] v = _values; byte[] states = _states; for ( int i = v.length, j = 0; i-- > 0; ) { if ( states[i] == FULL ) { vals[j++] = v[i]; } } return vals; }
/** {@inheritDoc} */ @Override public Object[] values() { Object[] vals = new Object[size()]; V[] v = _values; byte[] states = _states; for ( int i = v.length, j = 0; i-- > 0; ) { if ( states[i] == FULL ) { vals[j++] = v[i]; } } return vals; }
/** {@inheritDoc} */ @Override public long[] keys() { long[] keys = new long[size()]; long[] k = _set; byte[] states = _states; for ( int i = k.length, j = 0; i-- > 0; ) { if ( states[i] == FULL ) { keys[j++] = k[i]; } } return keys; }
/** {@inheritDoc} */ @SuppressWarnings({"unchecked"}) public long[] keys() { long[] keys = new long[size()]; long[] k = _set; byte[] states = _states; for ( int i = k.length, j = 0; i-- > 0; ) { if ( states[i] == FULL ) { keys[j++] = k[i]; } } return keys; }
/** {@inheritDoc} */ @SuppressWarnings({"unchecked"}) public Object[] values() { Object[] vals = new Object[size()]; V[] v = _values; byte[] states = _states; for ( int i = v.length, j = 0; i-- > 0; ) { if ( states[i] == FULL ) { vals[j++] = v[i]; } } return vals; }
/** {@inheritDoc} */ @SuppressWarnings({"unchecked"}) public long[] keys() { long[] keys = new long[size()]; long[] k = _set; byte[] states = _states; for ( int i = k.length, j = 0; i-- > 0; ) { if ( states[i] == FULL ) { keys[j++] = k[i]; } } return keys; }
public int getKmerCount() { return kmers.size(); } public Collection<Long> getAllKmers() { return Longs.asList(kmers.keys()); }
public int size() { return kmers.size(); } /**
public String toString(int maxNodesToPrint) { StringBuilder sb = new StringBuilder(); sb.append(String.format("De Bruijn graph: k=%d, %d kmers\n", k, kmers.size())); for (long x : kmers.keys()) { sb.append(printKmer(x)); maxNodesToPrint--; if (maxNodesToPrint <= 0) break; } return sb.toString(); } public String printKmer(long x) {
private static TLongObjectHashMap<CfHolder> multiplySparseUnivariate(IntegersZp64 ring, TLongObjectHashMap<CfHolder> a, TLongObjectHashMap<CfHolder> b) { TLongObjectHashMap<CfHolder> result = new TLongObjectHashMap<>(a.size() + b.size()); TLongObjectIterator<CfHolder> ait = a.iterator(); while (ait.hasNext()) { ait.advance(); TLongObjectIterator<CfHolder> bit = b.iterator(); while (bit.hasNext()) { bit.advance(); long deg = ait.key() + bit.key(); long val = ring.multiply(ait.value().coefficient, bit.value().coefficient); CfHolder r = result.putIfAbsent(deg, new CfHolder(val)); if (r != null) r.coefficient = ring.add(r.coefficient, val); } } return result; }