Examples with View org.cytoscape.view.model.View used on opensource projects

Example 31 with View

use of org.cytoscape.view.model.View in project cytoscape-impl by cytoscape.

the class EdgeBundlerTask method run.

@Override
public void run(TaskMonitor tm) {
    // Check tunables
    if (numNubs < 1)
        numNubs = 1;
    if (numNubs > 50) {
        logger.warn("Maximum handles is 50.");
        numNubs = 50;
    }
    tm.setTitle("Edge Bundle Layout");
    // Pre-cache data structures
    tm.setStatusMessage("Caching network data");
    Collection<View<CyEdge>> edges = null;
    // Get selection
    if (// Use all edges
    selection == 0) {
        edges = this.view.getEdgeViews();
    } else if (// Use selected nodes only
    selection == 1) {
        Collection<View<CyEdge>> edgeView = this.view.getEdgeViews();
        edges = new ArrayList<View<CyEdge>>(edgeView.size());
        for (View<CyEdge> e : edgeView) {
            boolean n1 = view.getNodeView(e.getModel().getSource()).getVisualProperty(EDGE_SELECTED);
            boolean n2 = view.getNodeView(e.getModel().getTarget()).getVisualProperty(EDGE_SELECTED);
            if (n1 && n2)
                edges.add(e);
        }
    } else if (// Use selected edges only
    selection == 2) {
        Collection<View<CyEdge>> edgeView = this.view.getEdgeViews();
        edges = new ArrayList<View<CyEdge>>(edgeView.size());
        for (View<CyEdge> e : edgeView) if (e.getVisualProperty(EDGE_SELECTED))
            edges.add(e);
    }
    int ei = 0;
    for (View<CyEdge> e : edges) {
        View<CyNode> eSource = view.getNodeView(e.getModel().getSource());
        View<CyNode> eTarget = view.getNodeView(e.getModel().getTarget());
        if (eSource.getSUID().equals(eTarget.getSUID()))
            continue;
        ei++;
    }
    numEdges = ei;
    if (numEdges < 2) {
        logger.warn("Less than two edges found.");
        return;
    }
    edgePos = new double[2][2][numEdges];
    nubs = new double[numNubs][2][numEdges];
    edgeLength = new double[numEdges];
    ei = 0;
    for (final View<CyEdge> e : edges) {
        // System.out.println("SUID: "+e.getModel().getSUID());
        View<CyNode> eSource = view.getNodeView(e.getModel().getSource());
        View<CyNode> eTarget = view.getNodeView(e.getModel().getTarget());
        if (eSource.getSUID().equals(eTarget.getSUID()))
            continue;
        edgePos[0][0][ei] = eSource.getVisualProperty(NODE_X_LOCATION);
        edgePos[0][1][ei] = eSource.getVisualProperty(NODE_Y_LOCATION);
        edgePos[1][0][ei] = eTarget.getVisualProperty(NODE_X_LOCATION);
        edgePos[1][1][ei] = eTarget.getVisualProperty(NODE_Y_LOCATION);
        double diffx = edgePos[1][0][ei] - edgePos[0][0][ei];
        double diffy = edgePos[1][1][ei] - edgePos[0][1][ei];
        for (int ni = 0; ni < numNubs; ni++) {
            nubs[ni][0][ei] = (diffx) * (ni + 1) / (numNubs + 1) + edgePos[0][0][ei];
            nubs[ni][1][ei] = (diffy) * (ni + 1) / (numNubs + 1) + edgePos[0][1][ei];
        }
        edgeLength[ei] = Math.sqrt(diffx * diffx + diffy * diffy);
        ei++;
    }
    computeEdgeCompatability();
    // Simulating physics
    tm.setStatusMessage("Simulating physics");
    double time = System.nanoTime();
    final double maxItrDouble = Double.valueOf(maxIterations);
    // Nub, X/Y, edgeIndex
    final double[][][] forces = new double[numNubs][2][numEdges];
    final HandleFactory handleFactory = serviceRegistrar.getService(HandleFactory.class);
    final BendFactory bendFactory = serviceRegistrar.getService(BendFactory.class);
    final VisualMappingManager visualMappingManager = serviceRegistrar.getService(VisualMappingManager.class);
    final VisualMappingFunctionFactory discreteFactory = serviceRegistrar.getService(VisualMappingFunctionFactory.class, "(mapping.type=discrete)");
    // Repeat the simulation [maxIterations] times.
    for (int iteri = 0; iteri < maxIterations; iteri++) {
        if (this.cancelled) {
            logger.info("Edge bundling cancelled: iter=" + iteri);
            break;
        }
        tm.setProgress(iteri / maxItrDouble);
        updateForces(forces);
        updateNubs(forces);
        // Check convergence once in awhile
        if (iteri % 1000 == 0 && isConverged(forces, .01)) {
            logger.info("Edge bundling converged: iter=" + iteri);
            break;
        }
        if (iteri == maxIterations - 1) {
            logger.info("Edge bundling did not converge: iter=" + iteri);
            break;
        }
        if (animate && System.nanoTime() - time > 3) {
            render(edges, handleFactory, bendFactory, visualMappingManager, discreteFactory);
            time = System.nanoTime();
        }
    }
    render(edges, handleFactory, bendFactory, visualMappingManager, discreteFactory);
}

Example 32 with View

use of org.cytoscape.view.model.View in project cytoscape-impl by cytoscape.

the class NodeChangeListener method updateGroupLocation.

private void updateGroupLocation(CyNetworkView networkView, View<CyNode> nodeView) {
    double groupX = nodeView.getVisualProperty(BasicVisualLexicon.NODE_X_LOCATION);
    double groupY = nodeView.getVisualProperty(BasicVisualLexicon.NODE_Y_LOCATION);
    CyGroup group = cyGroupManager.getGroup(nodeView.getModel(), networkView.getModel());
    if (group == null)
        return;
    // System.out.println("Updating group "+group+" location");
    Dimension lastPosition = ViewUtils.getLocation(networkView.getModel(), group);
    double xOffset = lastPosition.getWidth() - groupX;
    double yOffset = lastPosition.getHeight() - groupY;
    // System.out.println("Group node offset = "+xOffset+","+yOffset);
    List<View<CyNode>> groupNodeList = new ArrayList<>();
    boolean lastIgnoreChanges = ignoreChanges;
    ignoreChanges = true;
    // OK, move all of our nodes
    for (CyNode node : group.getNodeList()) {
        View<CyNode> nv = networkView.getNodeView(node);
        if (nv == null)
            continue;
        double x = nv.getVisualProperty(BasicVisualLexicon.NODE_X_LOCATION);
        double y = nv.getVisualProperty(BasicVisualLexicon.NODE_Y_LOCATION);
        // System.out.println("Node location = "+x+","+y);
        Dimension d = new Dimension();
        // System.out.println("Moving node to "+(x-xOffset)+","+(y-yOffset));
        d.setSize(x - xOffset, y - yOffset);
        ViewUtils.moveNode(networkView, node, d);
        if (cyGroupManager.isGroup(node, networkView.getModel()))
            groupNodeList.add(nv);
    }
    final CyEventHelper cyEventHelper = cyGroupManager.getService(CyEventHelper.class);
    cyEventHelper.flushPayloadEvents();
    ViewUtils.updateGroupLocation(networkView.getModel(), group, groupX, groupY);
    if (groupNodeList.size() > 0) {
        for (View<CyNode> nv : groupNodeList) {
            updateGroupLocation(networkView, nv);
        }
    }
    ignoreChanges = lastIgnoreChanges;
    cyEventHelper.flushPayloadEvents();
}

Example 33 with View

use of org.cytoscape.view.model.View in project cytoscape-impl by cytoscape.

the class GMLNetworkReader method layoutGraphics.

/**
 * Assigns visual properties to node and edge views, based on the values in
 * the GML "graphics" list.
 */
@SuppressWarnings("unchecked")
private void layoutGraphics(final CyNetworkView netView, final List<KeyValue> list, final View<? extends CyIdentifiable> view) {
    final CyIdentifiable model = view.getModel();
    Class<? extends CyIdentifiable> type = CyNetwork.class;
    if (model instanceof CyNode)
        type = CyNode.class;
    else if (model instanceof CyEdge)
        type = CyEdge.class;
    boolean srcArrowParsed = false;
    boolean tgtArrowParsed = false;
    for (final KeyValue keyVal : list) {
        String key = keyVal.key;
        Object value = keyVal.value;
        Object vpValue = null;
        if (type == CyNode.class) {
            if (key.equals(OUTLINE_WIDTH))
                key = WIDTH;
        } else if (type == CyEdge.class) {
            if (key.equals(LINE)) {
                // This is a polyline obj. However, it will be translated
                // into straight line.
                layoutEdgeGraphicsLine(netView, (List<KeyValue>) value, (View<CyEdge>) view);
                continue;
            }
            if (key.equals(YED_ARROW) && !(srcArrowParsed || tgtArrowParsed)) {
                if (value.toString().equals(ARROW_NONE))
                    continue;
                if (value.toString().equals(ARROW_FIRST))
                    key = YED_SOURCE_ARROW;
                else if (value.toString().equals(ARROW_LAST))
                    key = YED_TARGET_ARROW;
                vpValue = ArrowShapeVisualProperty.ARROW;
            } else {
                if (key.equals(YED_SOURCE_ARROW) || key.equals(YED_TARGET_ARROW)) {
                    vpValue = yedArrowShapes.get(value.toString());
                } else if (key.equals(SOURCE_ARROW) || key.equals(TARGET_ARROW)) {
                    key = key.replace("_arrow", "Arrow");
                    vpValue = legacyArrowShapes.get(value.toString());
                }
                if (key.equals(YED_SOURCE_ARROW))
                    srcArrowParsed = true;
                if (key.equals(YED_TARGET_ARROW))
                    tgtArrowParsed = true;
            }
        }
        final Set<VisualProperty<?>> vpSet = getVisualProperties(type, key);
        if (vpSet.isEmpty()) {
            unrecognizedVisualPropertyMgr.addUnrecognizedVisualProperty(netView, view, key, value.toString());
        } else {
            for (final VisualProperty<?> vp : vpSet) {
                if (vpValue == null)
                    vpValue = vp.parseSerializableString(value.toString());
                if (vpValue != null) {
                    if (isLockedVisualProperty(model, key)) {
                        // so we should avoid bypass.
                        if (vp != BasicVisualLexicon.NODE_LABEL) {
                            view.setLockedValue(vp, vpValue);
                        }
                    } else
                        view.setVisualProperty(vp, vpValue);
                }
            }
        }
    }
}

Example 34 with View

use of org.cytoscape.view.model.View in project cytoscape-impl by cytoscape.

the class GenericXGMMLReader method buildCyNetworkView.

@Override
public CyNetworkView buildCyNetworkView(final CyNetwork network) {
    NetworkViewRenderer networkViewRenderer = null;
    if (readDataMgr.getRendererId() != null)
        networkViewRenderer = cyApplicationManager.getNetworkViewRenderer(readDataMgr.getRendererId());
    // If the XGMML has no renderer ID info or a NetworkViewRenderer with that ID can't be found,
    // just use the passed CyNetworkViewFactory.
    // Otherwise use the factory provided by the specified NetworkViewRenderer.
    final CyNetworkViewFactory netViewFactory = networkViewRenderer != null ? networkViewRenderer.getNetworkViewFactory() : getNetworkViewFactory();
    final CyNetworkView netView = netViewFactory.createNetworkView(network);
    setNetworkViewProperties(netView);
    if (netView.getModel().getNodeCount() > 0) {
        final Collection<View<CyNode>> nodes = netView.getNodeViews();
        final Collection<View<CyEdge>> edges = netView.getEdgeViews();
        for (final View<CyNode> nodeView : nodes) setNodeViewProperties(netView, nodeView);
        for (final View<CyEdge> edgeView : edges) setEdgeViewProperties(netView, edgeView);
    }
    if (!readDataMgr.isSessionFormat())
        readDataMgr.updateGroupNodes(netView);
    return netView;
}

Example 35 with View

use of org.cytoscape.view.model.View in project PhenomeScape by soulj.

the class PhenomeExpress method run.

@Override
public void run(TaskMonitor taskMonitor) throws Exception {
    taskMonitor.setTitle("Running PhenomeExpress");
    taskMonitor.setStatusMessage("Preparing Networks");
    long time = System.currentTimeMillis();
    inputCheck();
    setUpNetworks();
    double[] relativeWeighting = { 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8 };
    double[] alphas = { 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8 };
    double[] piValues = proteinNetwork.getPivalues();
    Map<String, Integer> phenotypeMap = phenomeNetwork.getName2IndexMap();
    double[] phenoArray = new double[phenomeNetwork.getName2IndexMap().size()];
    selectedPhenotypes = new ArrayList<Phenotype>();
    boolean first = true;
    for (Phenotype phenotype : phenotypes) {
        if (phenotype.getSelected()) {
            if (first) {
                phenotypeSelected = phenotype.getID();
                phenotypeNamesSelected = phenotype.getName();
                selectedPhenotypes.add(phenotype);
                phenoArray[phenotypeMap.get(phenotype.getID())] = 1.0;
                first = false;
            } else {
                phenotypeSelected = phenotypeSelected + " ," + phenotype.getID();
                phenotypeNamesSelected = phenotypeNamesSelected + " ," + phenotype.getName();
                phenoArray[phenotypeMap.get(phenotype.getID())] = 1.0;
                selectedPhenotypes.add(phenotype);
            }
        }
    }
    Map<CyNode, Integer> map = proteinNetwork.getNode2IndexMap();
    int size = proteinNetwork.getNetwork().getNodeCount();
    int[] occuranceArray = new int[size];
    HashMap<CyNode, Protein> node2Protein = new HashMap<CyNode, Protein>();
    if (cancelled) {
        return;
    }
    taskMonitor.setStatusMessage("Calculating Activity Scores");
    taskMonitor.setProgress(0.0);
    double progress = 0.0;
    SparseRowMatrix adjMatrix = SparseRowMatrix.create(size, size);
    double[] transitionProbs = { 0.5, 0.6, 0.7, 0.8 };
    for (double transitionProb : transitionProbs) {
        TransitionMatrix transitionMatrix = new TransitionMatrix(phenomeNetwork.normalise(transitionProb, phenoGeneNetwork), proteinNetwork.normalise(transitionProb, phenoGeneNetwork), phenoGeneNetwork.normaliseT(transitionProb), phenoGeneNetwork.normalise(transitionProb));
        for (double weighting : relativeWeighting) {
            if (cancelled) {
                return;
            }
            transitionMatrix.prepareVector(piValues, phenoArray, weighting);
            for (double alpha : alphas) {
                progress += 0.0051;
                taskMonitor.setProgress(progress);
                double[] pageRankResults = transitionMatrix.pageRank(alpha);
                HashMap<Integer, Protein> index2ProteinMap = proteinNetwork.getIndex2ProteinMap();
                for (int i = 0; i < index2ProteinMap.size(); i++) {
                    Protein protein = index2ProteinMap.get(i);
                    protein.setValue(pageRankResults[i]);
                }
                List<Protein> proteinList = new ArrayList<Protein>(index2ProteinMap.values());
                Collections.sort(proteinList, new DescendingScoreComparator());
                int rank = 0;
                for (Protein protein : proteinList) {
                    rank++;
                    protein.setRank(rank);
                    node2Protein.put(protein.getNode(), protein);
                }
                Collections.sort(proteinList, new DescendingScoreComparator());
                GIGA giga = new GIGA(proteinList, node2Protein, proteinNetwork, maxNetworkSize);
                giga.compute();
                for (GIGACluster cluster : giga.getClusters()) {
                    for (CyNode node : cluster.getCluster()) {
                        Integer index = map.get(node);
                        AVector row = adjMatrix.getRow(index);
                        if (!row.isMutable()) {
                            row = row.mutable();
                        }
                        for (CyNode node2 : cluster.getCluster()) {
                            Integer index2 = map.get(node2);
                            row.set(index2, row.get(index2) + 1.0);
                            occuranceArray[index2]++;
                        }
                        adjMatrix.replaceRow(index, row);
                    }
                }
            }
        }
    }
    if (cancelled) {
        return;
    }
    taskMonitor.setProgress(1.0);
    taskMonitor.setStatusMessage("Creating Consensus Subnetworks");
    AMatrix cooccuranceMat = adjMatrix.transposeInnerProduct(adjMatrix);
    for (int i = 0; i < size; i++) {
        AVector row = cooccuranceMat.getRow(i);
        if (row.elementSum() > 0) {
            row.divide(occuranceArray[i]);
            Index nonSparse = row.nonSparseIndex();
            for (int j = 0; j < nonSparse.length(); j++) {
                if (row.get(nonSparse.get(j)) < 1.0) {
                    row.set(nonSparse.get(j), 0.0);
                }
            }
            cooccuranceMat.replaceRow(i, row.sparse());
        }
    }
    ConnectedComponentAnalyser CCA = new ConnectedComponentAnalyser(node2Protein);
    ArrayList<PhenomeExpressSubnetwork> subnetworks = CCA.ccFromAdjMatrix(adjMatrix, proteinNetwork);
    Iterator<PhenomeExpressSubnetwork> it = subnetworks.iterator();
    while (it.hasNext()) {
        PhenomeExpressSubnetwork subnetwork = it.next();
        if (subnetwork.getNodeList().size() < this.minNetSize) {
            it.remove();
        }
    }
    if (cancelled) {
        return;
    }
    taskMonitor.setStatusMessage("Calculating Subnetwork Significance");
    subnetworksSignificance(subnetworks);
    taskMonitor.setStatusMessage("Visualising Subnetworks");
    List<Double> foldChangeValues = proteinNetwork.getNodeTable().getColumn(foldChange).getValues(Double.class);
    double fcMax = Collections.max(foldChangeValues);
    double fcMin = Collections.min(foldChangeValues);
    // Apply the visual style to a NetworkView
    VizStyle vizStyle = new VizStyle();
    VisualStyle vs = vizStyle.createVizStyle(cyServiceRegistrar, geneName, foldChange, fcMax, fcMin);
    this.property = getNodeLabelPositionProperty();
    vs.setDefaultValue(property, property.parseSerializableString("N,S,c,0.0,0.0"));
    VisualMappingManager visualMappingManager = cyServiceRegistrar.getService(VisualMappingManager.class);
    visualMappingManager.setCurrentVisualStyle(vs);
    ArrayList<CyNetworkView> networkViewList = new ArrayList<CyNetworkView>();
    Iterator<PhenomeExpressSubnetwork> it2 = subnetworks.iterator();
    CyNetworkManager networkManager = cyServiceRegistrar.getService(CyNetworkManager.class);
    CyNetworkViewFactory networkViewFactory = cyServiceRegistrar.getService(CyNetworkViewFactory.class);
    CyLayoutAlgorithmManager layoutManager = cyServiceRegistrar.getService(CyLayoutAlgorithmManager.class);
    CyApplicationManager cyApplicationManager = cyServiceRegistrar.getService(CyApplicationManager.class);
    CyLayoutAlgorithm layout = layoutManager.getLayout("force-directed");
    Map<String, Object> settings = new HashMap<String, Object>();
    settings.put("defaultSpringLength", 5.0);
    settings.put("defaultSpringNodeMass", 2.0);
    TunableSetter setter = cyServiceRegistrar.getService(TunableSetter.class);
    Object context = layout.createLayoutContext();
    setter.applyTunables(context, settings);
    GOTermAnalyser2 goTermAnalyser = new GOTermAnalyser2(proteinNetwork, species);
    while (it2.hasNext()) {
        PhenomeExpressSubnetwork subnet = it2.next();
        if (subnet.getPvalue() > this.threshold) {
            it2.remove();
        } else {
            goTermAnalyser.calculateGOTermPValues(subnet, proteinNetwork);
            String subnetworkName = NetworkUtils.getUniqueNetworkName(cyServiceRegistrar, networkName + "_" + subnet.getBestGOTerm());
            subnet.setName(subnetworkName);
            CySubNetwork subnetwork = NetworkUtils.createSubNetwork(((CySubNetwork) proteinNetwork.getNetwork()).getRootNetwork(), subnet.getNodeList());
            subnetwork.getRow(subnetwork).set(CyNetwork.NAME, subnetworkName);
            addSeedPhenotypes(subnetwork);
            networkManager.addNetwork(subnetwork);
            CyNetworkViewManager viewManager = cyServiceRegistrar.getService(CyNetworkViewManager.class);
            CyNetworkView nv = networkViewFactory.createNetworkView(subnetwork);
            viewManager.addNetworkView(nv);
            cyApplicationManager.setCurrentNetworkView(nv);
            for (CyNode phenoNode : phenotypesAdded) {
                View<CyNode> nodeView = nv.getNodeView(phenoNode);
                nodeView.setLockedValue(BasicVisualLexicon.NODE_SHAPE, NodeShapeVisualProperty.RECTANGLE);
                nodeView.setLockedValue(BasicVisualLexicon.NODE_FILL_COLOR, Color.BLUE);
            }
            for (CyEdge phenoEdge : phenoEdges) {
                View<CyEdge> edgeView = nv.getEdgeView(phenoEdge);
                edgeView.setLockedValue(BasicVisualLexicon.EDGE_LINE_TYPE, LineTypeVisualProperty.DOT);
                edgeView.setLockedValue(BasicVisualLexicon.EDGE_PAINT, Color.BLUE);
            }
            networkViewList.add(nv);
            Set<View<CyNode>> nodeSet = Collections.emptySet();
            cyServiceRegistrar.getService(TaskManager.class).execute(layout.createTaskIterator(nv, context, nodeSet, null));
        }
    }
    CyEventHelper cyEventHelper = cyServiceRegistrar.getService(CyEventHelper.class);
    for (CyNetworkView nv : networkViewList) {
        visualMappingManager.setVisualStyle(vs, nv);
        vs.apply(nv);
        cyEventHelper.flushPayloadEvents();
        cyApplicationManager.setCurrentNetworkView(nv);
        nv.updateView();
    }
    phenomeNetwork = null;
    proteinNetwork = null;
    ResultsPanel resultsPanel = (ResultsPanel) CytoPanelUtils.getCytoPanel(cyServiceRegistrar, ResultsPanel.class, CytoPanelName.EAST);
    resultsPanel.newTableData(getResultsSummary(subnetworks), getParameterList());
    CytoPanelUtils.showCytoPanel(cyServiceRegistrar, CytoPanelName.EAST);
}