List of usage examples for java.util HashSet removeIf
default boolean removeIf(Predicate<? super E> filter)
From source file:blusunrize.immersiveengineering.api.ApiUtils.java
private static boolean handlePos(Vec3d pos, BlockPos posB, HashMap<BlockPos, Vec3d> halfScanned, HashSet<BlockPos> done, Predicate<Triple<BlockPos, Vec3d, Vec3d>> shouldStop, HashSet<Triple<BlockPos, Vec3d, Vec3d>> near) { final double DELTA_NEAR = .3; if (!done.contains(posB)) { if (halfScanned.containsKey(posB) && !pos.equals(halfScanned.get(posB))) { Triple<BlockPos, Vec3d, Vec3d> added = new ImmutableTriple<>(posB, halfScanned.get(posB), pos); boolean stop = shouldStop.test(added); done.add(posB);// w w w.jav a 2 s. co m halfScanned.remove(posB); near.removeIf((t) -> t.getLeft().equals(posB)); if (stop) return true; for (int i = 0; i < 3; i++) { double coord = getDim(pos, i); double diff = coord - Math.floor(coord); if (diff < DELTA_NEAR) near.add( new ImmutableTriple<>(offsetDim(posB, i, -1), added.getMiddle(), added.getRight())); diff = Math.ceil(coord) - coord; if (diff < DELTA_NEAR) near.add(new ImmutableTriple<>(offsetDim(posB, i, 1), added.getMiddle(), added.getRight())); } } else { halfScanned.put(posB, pos); } } return false; }
From source file:com.net2plan.gui.utils.topologyPane.jung.JUNGCanvas.java
/** * Default constructor.//from w w w . j a va2s . co m * * @since 0.2.3 */ public JUNGCanvas(IVisualizationCallback callback, TopologyPanel topologyPanel) { this.callback = callback; transformNetPlanCoordinatesToJungCoordinates = vertex -> { final int vlIndex = this.callback.getVisualizationState() .getCanvasVisualizationOrderRemovingNonVisible(vertex.getLayer()); final double interLayerDistanceInNpCoord = currentInterLayerDistanceInNpCoordinates; final Point2D basePositionInNetPlanCoord = vertex.getAssociatedNetPlanNode().getXYPositionMap(); return new Point2D.Double(basePositionInNetPlanCoord.getX(), -(basePositionInNetPlanCoord.getY() + (vlIndex * interLayerDistanceInNpCoord))); }; g = new DirectedOrderedSparseMultigraph<>(); l = new StaticLayout<>(g, transformNetPlanCoordinatesToJungCoordinates); vv = new VisualizationViewer<>(l); osmStateManager = new OSMStateManager(callback, topologyPanel, this); originalEdgeShapeTransformer = new EdgeShape.QuadCurve<>(); ((EdgeShape.QuadCurve<GUINode, GUILink>) originalEdgeShapeTransformer).setControlOffsetIncrement(10); // how much they separate from the direct line (default is 20) //((EdgeShape.QuadCurve<GUINode, GUILink>) originalEdgeShapeTransformer).setEdgeIndexFunction(DefaultParallelEdgeIndexFunction.<GUINode, GUILink>getInstance()); // how much they separate from the direct line (default is 20) /* This functions gives an index to the links to show separate (curved): the order among the parallel links (BUT NOW only among the separated ones among them) */ ((EdgeShape.QuadCurve<GUINode, GUILink>) originalEdgeShapeTransformer) .setEdgeIndexFunction(new EdgeIndexFunction<GUINode, GUILink>() { public void reset(Graph<GUINode, GUILink> graph, GUILink e) { } public void reset() { } public int getIndex(Graph<GUINode, GUILink> graph, GUILink e) { final GUINode u = e.getOriginNode(); final GUINode v = e.getDestinationNode(); final HashSet<GUILink> commonEdgeSet = new HashSet<>(graph.getInEdges(v)); commonEdgeSet.retainAll(graph.getOutEdges(u)); commonEdgeSet.removeIf(ee -> !ee.isShownSeparated()); int count = 0; for (GUILink other : commonEdgeSet) if (other == e) return count; else count++; throw new RuntimeException(); } }); /* Customize the graph */ vv.getRenderContext().setVertexDrawPaintTransformer(n -> n.getDrawPaint()); vv.getRenderContext().setVertexFillPaintTransformer(n -> n.getFillPaint()); vv.getRenderContext().setVertexFontTransformer(n -> n.getFont()); vv.getRenderContext().setVertexIconTransformer(gn -> gn.getIcon()); vv.getRenderContext().setVertexIncludePredicate( guiNodeContext -> callback.getVisualizationState().isVisibleInCanvas(guiNodeContext.element)); vv.getRenderer().setVertexLabelRenderer(new NodeLabelRenderer()); vv.setVertexToolTipTransformer(node -> node.getToolTip()); vv.getRenderContext().setEdgeIncludePredicate( context -> callback.getVisualizationState().isVisibleInCanvas(context.element)); vv.getRenderContext().setEdgeArrowPredicate( context -> callback.getVisualizationState().isVisibleInCanvas(context.element) && context.element.getHasArrow()); vv.getRenderContext().setEdgeArrowStrokeTransformer(i -> i.getArrowStroke()); vv.getRenderContext() .setEdgeArrowTransformer(new ConstantTransformer(ArrowFactory.getNotchedArrow(7, 10, 5))); vv.getRenderContext().setEdgeLabelClosenessTransformer(new ConstantDirectionalEdgeValueTransformer(.6, .6)); vv.getRenderContext().setEdgeStrokeTransformer(i -> i.getEdgeStroke()); vv.getRenderContext().setEdgeDrawPaintTransformer(e -> e.getEdgeDrawPaint()); vv.getRenderContext().setArrowDrawPaintTransformer(e -> e.getArrowDrawPaint()); vv.getRenderContext().setArrowFillPaintTransformer(e -> e.getArrowFillPaint()); vv.getRenderContext().setEdgeLabelRenderer(new DefaultEdgeLabelRenderer(Color.BLUE)); vv.getRenderer().setEdgeLabelRenderer(new BasicEdgeLabelRenderer<GUINode, GUILink>() { public void labelEdge(RenderContext<GUINode, GUILink> rc, Layout<GUINode, GUILink> layout, GUILink e, String label) { if (callback.getVisualizationState().isCanvasShowLinkLabels()) super.labelEdge(rc, layout, e, e.getLabel()); } }); vv.setEdgeToolTipTransformer(link -> link.getToolTip()); vv.getRenderContext().setEdgeShapeTransformer( c -> c.element.isShownSeparated() ? originalEdgeShapeTransformer.transform(c) : new Line2D.Float(0.0f, 0.0f, 1.0f, 0.0f)); // Background controller this.paintableAssociatedToBackgroundImage = null; gm = new PluggableGraphMouse(); vv.setGraphMouse(gm); scalingControl = new LayoutScalingControl(); ITopologyCanvasPlugin scalingPlugin = new ScalingCanvasPlugin(scalingControl, MouseEvent.NOBUTTON); addPlugin(scalingPlugin); vv.setOpaque(false); vv.setBackground(new Color(0, 0, 0, 0)); this.updateInterLayerDistanceInNpCoordinates(callback.getVisualizationState().getInterLayerSpaceInPixels()); // reset(); }
From source file:gedi.riboseq.inference.orf.OrfFinder.java
/** * Coordinates are in codonsRegion space! * @param index//from w w w .jav a2 s. c om * @param sequence * @param sg * @param codonsRegion * @return */ public ArrayList<OrfWithCodons> findOrfs(int index, String sequence, SpliceGraph sg, ImmutableReferenceGenomicRegion<IntervalTreeSet<Codon>> codonsRegion) { SimpleDirectedGraph<Codon> fg = new SimpleDirectedGraph<Codon>("Codongraph"); // if (!codonsRegion.getReference().toString().equals("chr4+") || !codonsRegion.getRegion().contains(140_283_087)) // return 0; LeftMostInFrameAndClearList buff = new LeftMostInFrameAndClearList(); IntervalTreeSet<Codon> codons = codonsRegion.getData(); codons.removeIf(c -> c.getTotalActivity() < minCodonActivity); if (codons.size() == 0) return new ArrayList<OrfWithCodons>(); // add stop codons for easy orf inference HashSet<Codon> stopCodons = new HashSet<Codon>(); Trie<String> stop = new Trie<String>(); stop.put("TAG", "TAG"); stop.put("TGA", "TGA"); stop.put("TAA", "TAA"); stop.iterateAhoCorasick(sequence) .map(r -> new Codon(new ArrayGenomicRegion(r.getStart(), r.getEnd()), r.getValue())) .toCollection(stopCodons); for (Intron intr : sg.iterateIntrons().loop()) { ArrayGenomicRegion reg = new ArrayGenomicRegion(intr.getStart() - 2, intr.getStart(), intr.getEnd(), intr.getEnd() + 1); String cod = stop.get(SequenceUtils.extractSequence(reg, sequence)); if (cod != null) stopCodons.add(new Codon(reg, cod)); reg = new ArrayGenomicRegion(intr.getStart() - 1, intr.getStart(), intr.getEnd(), intr.getEnd() + 2); cod = stop.get(SequenceUtils.extractSequence(reg, sequence)); if (cod != null) stopCodons.add(new Codon(reg, cod)); } stopCodons.removeAll(codons); codons.addAll(stopCodons); ArrayList<OrfWithCodons> re = new ArrayList<OrfWithCodons>(); HashSet<Codon> usedForAnno = new HashSet<Codon>(); if (assembleAnnotationFirst) { // new: first use annotated transcripts in a greedy fashion ArrayList<ImmutableReferenceGenomicRegion<Transcript>> transcripts = annotation.ei(codonsRegion) .filter(t -> t.getData().isCoding()).map(t -> codonsRegion.induce(t, "T")).list(); int acount = 0; LinkedList<OrfWithCodons> orfs = new LinkedList<OrfWithCodons>(); GenomicRegion best; HashSet<Codon> aremoved = new HashSet<Codon>(); do { best = null; double bestSum = 0; for (ImmutableReferenceGenomicRegion<Transcript> tr : transcripts) { double[] a = new double[tr.getRegion().getTotalLength()]; for (Codon c : codons) { if (tr.getRegion().containsUnspliced(c)) { int p = tr.induce(c.getStart()); assert a[p] == 0; if (!aremoved.contains(c)) a[p] = c.totalActivity; if (c.isStop()) a[p] = -1; } } for (int f = 0; f < 3; f++) { int s = -1; double sum = 0; for (int p = f; p < a.length; p += 3) { if (a[p] == -1) {//stop if (sum > bestSum) { bestSum = sum; best = tr.getRegion().map(new ArrayGenomicRegion(s, p + 3)); } s = -1; sum = 0; } else sum += a[p]; if (a[p] > 0 && s == -1) s = p; } } } if (best != null) { ArrayList<Codon> cods = new ArrayList<>(); int uniqueCodons = 0; double uniqueActivity = 0; double totalActivity = 0; for (Codon c : codons) { if (best.containsUnspliced(c) && best.induce(c.getStart()) % 3 == 0) { if (aremoved.add(c)) { uniqueActivity += c.totalActivity; uniqueCodons++; } totalActivity += c.totalActivity; if (c.totalActivity > 0) cods.add(c); } } // System.out.println(codonsRegion.map(best)); if ((uniqueCodons >= minUniqueCodons || uniqueCodons == cods.size()) && uniqueActivity > minUniqueActivity && totalActivity > minOrfTotalActivity) { Collections.sort(cods); usedForAnno.addAll(cods); OrfWithCodons orf = new OrfWithCodons(index, 0, acount++, best.toArrayGenomicRegion(), cods, true); orfs.add(orf); } } } while (best != null); if (orfs.size() > 1) { // they are not necessarily connected! LinkedList<OrfWithCodons>[] connected = findConnectedOrfs(orfs); orfs.clear(); for (LinkedList<OrfWithCodons> corfs : connected) { for (boolean changed = true; changed && corfs.size() > 1;) { changed = false; if (useEM) inferOverlappingOrfActivitiesEM(corfs); else overlapUniqueCoverage(corfs); Iterator<OrfWithCodons> it = corfs.iterator(); while (it.hasNext()) { OrfWithCodons orf = it.next(); if (orf.getEstimatedTotalActivity() < minOrfTotalActivity) { it.remove(); changed = true; } } } if (corfs.size() > 1) distributeCodons(corfs); orfs.addAll(corfs); } } re.addAll(orfs); } // as edges only are represented in the splice graph, singleton codons are discarded (which does make sense anyway) for (Codon c : codons) { if (!c.isStop()) { // find unspliced successors (can be more than one, when the successor codon itself is spliced! all of them have the same start!) int max = c.getEnd() + maxAminoDist * 3; for (Codon n : codons .getIntervalsIntersecting(c.getEnd(), c.getEnd() + maxAminoDist * 3, buff.startAndClear(c)) .get()) { if (!containsInframeStop(sequence.substring(c.getEnd(), n.getStart()))) fg.addInteraction(c, n); max = n.getStart() + 2; } // find all spliced successors for each splice junction that comes before n or maxAminoDist sg.forEachIntronStartingBetween(c.getEnd(), max + 1, intron -> { for (Codon n : codons.getIntervalsIntersecting(intron.getEnd(), intron.getEnd() + maxAminoDist * 3 - (intron.getStart() - c.getEnd()), buff.startAndClear(c, intron)).get()) if (!containsInframeStop(SequenceUtils.extractSequence(new ArrayGenomicRegion(c.getStart(), intron.getStart(), intron.getEnd(), n.getStart()), sequence))) fg.addInteraction(c, n, intron); }); } } int cc = 1; for (SimpleDirectedGraph<Codon> g : fg.getWeaklyConnectedComponents()) { if (EI.wrap(g.getSources()).mapToDouble(c -> c.getTotalActivity()).sum() == 0) continue; // iterate longest paths in g LinkedList<Codon> topo = g.getTopologicalOrder(); HashSet<Codon> remInTopo = new HashSet<Codon>(topo); remInTopo.removeIf(c -> !stopCodons.contains(c) && !usedForAnno.contains(c)); HashSet<Codon> removed = new HashSet<Codon>(remInTopo); // double maxPathScore = 0; LinkedList<OrfWithCodons> orfs = new LinkedList<OrfWithCodons>(); int count = 0; while (removed.size() < topo.size()) { HashMap<Codon, MutablePair<GenomicRegion, Double>> longestPrefixes = new HashMap<Codon, MutablePair<GenomicRegion, Double>>(); for (Codon c : topo) longestPrefixes.put(c, new MutablePair<GenomicRegion, Double>(c, removed.contains(c) ? 0 : (c.getTotalActivity()))); Codon longestEnd = null; HashMap<Codon, Codon> backtracking = new HashMap<Codon, Codon>(); for (Codon c : topo) { // if (codonsRegion.map(c).getStart()==100_466_118) // System.out.println(c); // // if (codonsRegion.map(c).getStart()==100_465_842) // System.out.println(c); double len = longestPrefixes.get(c).Item2; for (AdjacencyNode<Codon> n = g.getTargets(c); n != null; n = n.next) { MutablePair<GenomicRegion, Double> pref = longestPrefixes.get(n.node); double nnact = removed.contains(n.node) ? 0 : (n.node.getTotalActivity()); if (pref.Item2 <= len + nnact) { pref.set(extendFullPath(longestPrefixes.get(c).Item1, c, n.node, n.getLabel()), len + nnact); backtracking.put(n.node, c); } } if (longestEnd == null || longestPrefixes.get(longestEnd).Item2 <= len) longestEnd = c; } // determine longest path by backtracking and mark all codons on the path as removed ArrayList<Codon> orfCodons = new ArrayList<Codon>(); double totalActivity = 0; double uniqueActivity = 0; int uniqueCodons = 0; for (Codon c = longestEnd; c != null; c = backtracking.get(c)) { if (removed.add(c) && c.getTotalActivity() > 0) { uniqueCodons++; uniqueActivity += c.getTotalActivity(); } if (c.getTotalActivity() > 0) // to remove dummy stop codons orfCodons.add(c); totalActivity += c.getTotalActivity(); } // System.out.println(codonsRegion.map(longestPrefixes.get(longestEnd).Item1)); if ((uniqueCodons >= minUniqueCodons || uniqueCodons == orfCodons.size()) && uniqueActivity > minUniqueActivity && totalActivity > minOrfTotalActivity) { Collections.reverse(orfCodons); MutablePair<GenomicRegion, Double> triple = longestPrefixes.get(longestEnd); ArrayGenomicRegion region = triple.Item1.toArrayGenomicRegion(); String lastCodon = SequenceUtils.extractSequence( region.map( new ArrayGenomicRegion(region.getTotalLength() - 3, region.getTotalLength())), sequence); OrfWithCodons orf = new OrfWithCodons(index, cc, count++, region, orfCodons, stop.containsKey(lastCodon)); orfs.add(orf); } // maxPathScore = Math.max(maxPathScore,totalActivity); } if (orfs.size() > 1) { // they are not necessarily connected! LinkedList<OrfWithCodons>[] connected = findConnectedOrfs(orfs); orfs.clear(); for (LinkedList<OrfWithCodons> corfs : connected) { for (boolean changed = true; changed && corfs.size() > 1;) { changed = false; if (useEM) inferOverlappingOrfActivitiesEM(corfs); else overlapUniqueCoverage(corfs); Iterator<OrfWithCodons> it = corfs.iterator(); while (it.hasNext()) { OrfWithCodons orf = it.next(); if (orf.getEstimatedTotalActivity() < minOrfTotalActivity) { it.remove(); changed = true; } } } if (corfs.size() > 1) distributeCodons(corfs); orfs.addAll(corfs); } } re.addAll(orfs); cc++; } return re; }
From source file:org.apache.sysml.hops.codegen.opt.PlanSelectionFuseCostBased.java
private void createAndAddMultiAggPlans(CPlanMemoTable memo, ArrayList<Hop> roots) { //collect full aggregations as initial set of candidates HashSet<Long> fullAggs = new HashSet<>(); Hop.resetVisitStatus(roots);/*from www . ja va 2 s . co m*/ for (Hop hop : roots) rCollectFullAggregates(hop, fullAggs); Hop.resetVisitStatus(roots); //remove operators with assigned multi-agg plans fullAggs.removeIf(p -> memo.contains(p, TemplateType.MAGG)); //check applicability for further analysis if (fullAggs.size() <= 1) return; if (LOG.isTraceEnabled()) { LOG.trace("Found across-partition ua(RC) aggregations: " + Arrays.toString(fullAggs.toArray(new Long[0]))); } //collect information for all candidates //(subsumed aggregations, and inputs to fused operators) List<AggregateInfo> aggInfos = new ArrayList<>(); for (Long hopID : fullAggs) { Hop aggHop = memo.getHopRefs().get(hopID); AggregateInfo tmp = new AggregateInfo(aggHop); for (int i = 0; i < aggHop.getInput().size(); i++) { Hop c = HopRewriteUtils.isMatrixMultiply(aggHop) && i == 0 ? aggHop.getInput().get(0).getInput().get(0) : aggHop.getInput().get(i); rExtractAggregateInfo(memo, c, tmp, TemplateType.CELL); } if (tmp._fusedInputs.isEmpty()) { if (HopRewriteUtils.isMatrixMultiply(aggHop)) { tmp.addFusedInput(aggHop.getInput().get(0).getInput().get(0).getHopID()); tmp.addFusedInput(aggHop.getInput().get(1).getHopID()); } else tmp.addFusedInput(aggHop.getInput().get(0).getHopID()); } aggInfos.add(tmp); } if (LOG.isTraceEnabled()) { LOG.trace("Extracted across-partition ua(RC) aggregation info: "); for (AggregateInfo info : aggInfos) LOG.trace(info); } //sort aggregations by num dependencies to simplify merging //clusters of aggregations with parallel dependencies aggInfos = aggInfos.stream().sorted(Comparator.comparing(a -> a._inputAggs.size())) .collect(Collectors.toList()); //greedy grouping of multi-agg candidates boolean converged = false; while (!converged) { AggregateInfo merged = null; for (int i = 0; i < aggInfos.size(); i++) { AggregateInfo current = aggInfos.get(i); for (int j = i + 1; j < aggInfos.size(); j++) { AggregateInfo that = aggInfos.get(j); if (current.isMergable(that)) { merged = current.merge(that); aggInfos.remove(j); j--; } } } converged = (merged == null); } if (LOG.isTraceEnabled()) { LOG.trace("Merged across-partition ua(RC) aggregation info: "); for (AggregateInfo info : aggInfos) LOG.trace(info); } //construct and add multiagg template plans (w/ max 3 aggregations) for (AggregateInfo info : aggInfos) { if (info._aggregates.size() <= 1) continue; Long[] aggs = info._aggregates.keySet().toArray(new Long[0]); MemoTableEntry me = new MemoTableEntry(TemplateType.MAGG, aggs[0], aggs[1], (aggs.length > 2) ? aggs[2] : -1, aggs.length); for (int i = 0; i < aggs.length; i++) { memo.add(memo.getHopRefs().get(aggs[i]), me); addBestPlan(aggs[i], me); if (LOG.isTraceEnabled()) LOG.trace("Added multiagg* plan: " + aggs[i] + " " + me); } } }
From source file:org.apache.sysml.hops.codegen.template.PlanSelectionFuseCostBased.java
private void createAndAddMultiAggPlans(CPlanMemoTable memo, ArrayList<Hop> roots) { //collect full aggregations as initial set of candidates HashSet<Long> fullAggs = new HashSet<Long>(); Hop.resetVisitStatus(roots);// w ww .j a v a2 s . com for (Hop hop : roots) rCollectFullAggregates(hop, fullAggs); Hop.resetVisitStatus(roots); //remove operators with assigned multi-agg plans fullAggs.removeIf(p -> memo.contains(p, TemplateType.MultiAggTpl)); //check applicability for further analysis if (fullAggs.size() <= 1) return; if (LOG.isTraceEnabled()) { LOG.trace("Found across-partition ua(RC) aggregations: " + Arrays.toString(fullAggs.toArray(new Long[0]))); } //collect information for all candidates //(subsumed aggregations, and inputs to fused operators) List<AggregateInfo> aggInfos = new ArrayList<AggregateInfo>(); for (Long hopID : fullAggs) { Hop aggHop = memo._hopRefs.get(hopID); AggregateInfo tmp = new AggregateInfo(aggHop); for (int i = 0; i < aggHop.getInput().size(); i++) { Hop c = HopRewriteUtils.isMatrixMultiply(aggHop) && i == 0 ? aggHop.getInput().get(0).getInput().get(0) : aggHop.getInput().get(i); rExtractAggregateInfo(memo, c, tmp, TemplateType.CellTpl); } if (tmp._fusedInputs.isEmpty()) { if (HopRewriteUtils.isMatrixMultiply(aggHop)) { tmp.addFusedInput(aggHop.getInput().get(0).getInput().get(0).getHopID()); tmp.addFusedInput(aggHop.getInput().get(1).getHopID()); } else tmp.addFusedInput(aggHop.getInput().get(0).getHopID()); } aggInfos.add(tmp); } if (LOG.isTraceEnabled()) { LOG.trace("Extracted across-partition ua(RC) aggregation info: "); for (AggregateInfo info : aggInfos) LOG.trace(info); } //sort aggregations by num dependencies to simplify merging //clusters of aggregations with parallel dependencies aggInfos = aggInfos.stream().sorted(Comparator.comparing(a -> a._inputAggs.size())) .collect(Collectors.toList()); //greedy grouping of multi-agg candidates boolean converged = false; while (!converged) { AggregateInfo merged = null; for (int i = 0; i < aggInfos.size(); i++) { AggregateInfo current = aggInfos.get(i); for (int j = i + 1; j < aggInfos.size(); j++) { AggregateInfo that = aggInfos.get(j); if (current.isMergable(that)) { merged = current.merge(that); aggInfos.remove(j); j--; } } } converged = (merged == null); } if (LOG.isTraceEnabled()) { LOG.trace("Merged across-partition ua(RC) aggregation info: "); for (AggregateInfo info : aggInfos) LOG.trace(info); } //construct and add multiagg template plans (w/ max 3 aggregations) for (AggregateInfo info : aggInfos) { if (info._aggregates.size() <= 1) continue; Long[] aggs = info._aggregates.keySet().toArray(new Long[0]); MemoTableEntry me = new MemoTableEntry(TemplateType.MultiAggTpl, aggs[0], aggs[1], (aggs.length > 2) ? aggs[2] : -1); for (int i = 0; i < aggs.length; i++) { memo.add(memo._hopRefs.get(aggs[i]), me); addBestPlan(aggs[i], me); if (LOG.isTraceEnabled()) LOG.trace("Added multiagg* plan: " + aggs[i] + " " + me); } } }