private void checkView(final CyNetworkView view) {
    assertEquals(Color.BLACK, view.getVisualProperty(NETWORK_BACKGROUND_PAINT));
    assertEquals(new Double(639.0d), view.getVisualProperty(NETWORK_WIDTH));
    assertEquals(new Double(624.0d), view.getVisualProperty(NETWORK_HEIGHT));
    assertEquals(
        new Double(3091.2991395970175d), view.getVisualProperty(NETWORK_CENTER_X_LOCATION));
    assertEquals(new Double(3610.396738076269d), view.getVisualProperty(NETWORK_CENTER_Y_LOCATION));
    assertEquals(new Double(0.05044042295795177d), view.getVisualProperty(NETWORK_SCALE_FACTOR));

    // All nodes have the same size, border and shape
    final View<CyNode> nv = view.getNodeView(view.getModel().getNodeList().iterator().next());
    assertEquals(80, nv.getVisualProperty(NODE_WIDTH).intValue());
    assertEquals(30, nv.getVisualProperty(NODE_HEIGHT).intValue());
    assertEquals(NodeShapeVisualProperty.ROUND_RECTANGLE, nv.getVisualProperty(NODE_SHAPE));
    assertEquals(180, nv.getVisualProperty(NODE_TRANSPARENCY).intValue());
    assertEquals(2, nv.getVisualProperty(NODE_BORDER_WIDTH).intValue());
    assertEquals(LineTypeVisualProperty.SOLID, nv.getVisualProperty(NODE_BORDER_LINE_TYPE));
    assertEquals(new Color(153, 153, 255), nv.getVisualProperty(NODE_BORDER_PAINT));
    assertEquals(255, nv.getVisualProperty(NODE_BORDER_TRANSPARENCY).intValue());
    assertEquals(new Color(255, 255, 255), nv.getVisualProperty(NODE_LABEL_COLOR));
    assertEquals(255, nv.getVisualProperty(NODE_LABEL_TRANSPARENCY).intValue());

    // All edges have the same width and other properties
    final View<CyEdge> ev = view.getEdgeView(view.getModel().getEdgeList().iterator().next());
    assertEquals(new Double(1.0), ev.getVisualProperty(EDGE_WIDTH));
    assertEquals(255, ev.getVisualProperty(EDGE_TRANSPARENCY).intValue());
    assertEquals(ArrowShapeVisualProperty.NONE, ev.getVisualProperty(EDGE_SOURCE_ARROW_SHAPE));
    assertEquals(ArrowShapeVisualProperty.NONE, ev.getVisualProperty(EDGE_TARGET_ARROW_SHAPE));
  }
Ejemplo n.º 2
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  /**
   * By passing a list of key-value pairs for each Visual Property, update network view.
   *
   * <p>The body should have the following JSON:
   *
   * <pre>
   * [
   * 		{
   * 			"visualProperty": "Visual Property Name, like NETWORK_BACKGROUND_PAINT",
   * 			"value": "Serialized form of value, like 'red.'"
   * 		},
   * 		...
   * 		{}
   * ]
   * </pre>
   *
   * Note that this API directly set the value to the view objects, and once Visual Style applied,
   * those values are overridden by the Visual Style.
   *
   * @summary Update single network view value, such as background color or zoom level.
   * @param networkId Network SUID
   * @param viewId Network view SUID
   */
  @PUT
  @Path("/{viewId}/network")
  @Consumes(MediaType.APPLICATION_JSON)
  public Response updateNetworkView(
      @PathParam("networkId") Long networkId,
      @PathParam("viewId") Long viewId,
      final InputStream is) {
    final CyNetworkView networkView = getView(networkId, viewId);
    final ObjectMapper objMapper = new ObjectMapper();

    try {
      // This should be an JSON array.
      final JsonNode rootNode = objMapper.readValue(is, JsonNode.class);
      styleMapper.updateView(networkView, rootNode, getLexicon());
    } catch (Exception e) {
      throw getError(
          "Could not parse the input JSON for updating view because: " + e.getMessage(),
          e,
          Response.Status.INTERNAL_SERVER_ERROR);
    }
    // Repaint
    networkView.updateView();

    return Response.ok().build();
  }
Ejemplo n.º 3
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  /**
   * To use this API, you need to know SUID of the CyNetworkView, in addition to CyNetwork SUID.
   *
   * @summary Get a network view (as JSON or a file)
   * @param networkId Network SUID
   * @param viewId Network View SUID
   * @param file (Optional) If you want to get the view as a file, you can specify output file name
   *     with extension. For example, file=test.sif creates new SIF file in the current directory.
   * @return View in Cytoscape.js JSON. Currently, view information is (x, y) location only. If you
   *     specify <strong>file</strong> option, this returns absolute path to the file.
   */
  @GET
  @Path("/{viewId}")
  @Produces(MediaType.APPLICATION_JSON)
  public Response getNetworkView(
      @PathParam("networkId") Long networkId,
      @PathParam("viewId") Long viewId,
      @QueryParam("file") String file) {
    final Collection<CyNetworkView> views = this.getCyNetworkViews(networkId);

    CyNetworkView targetView = null;
    for (final CyNetworkView view : views) {
      final Long vid = view.getSUID();
      if (vid.equals(viewId)) {
        targetView = view;
        break;
      }
    }

    if (targetView == null) {
      return Response.ok("{}").build();
    } else {
      if (file != null) {
        return Response.ok(writeNetworkFile(file, targetView)).build();
      } else {
        return Response.ok(getNetworkViewString(targetView)).build();
      }
    }
  }
Ejemplo n.º 4
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  @GET
  @Path("/{viewId}/{objectType}/{objectId}/{visualProperty}")
  @Produces(MediaType.APPLICATION_JSON)
  public String getSingleVisualPropertyValue(
      @PathParam("networkId") Long networkId,
      @PathParam("viewId") Long viewId,
      @PathParam("objectType") String objectType,
      @PathParam("objectId") Long objectId,
      @PathParam("visualProperty") String visualProperty) {
    final CyNetworkView networkView = getView(networkId, viewId);

    Collection<VisualProperty<?>> vps = null;
    View<? extends CyIdentifiable> view = null;
    if (nodeLexicon == null) {
      initLexicon();
    }

    if (objectType.equals("nodes")) {
      view = networkView.getNodeView(networkView.getModel().getNode(objectId));
      vps = nodeLexicon;
    } else if (objectType.equals("edges")) {
      view = networkView.getNodeView(networkView.getModel().getNode(objectId));
      vps = edgeLexicon;
    }

    if (view == null) {
      throw getError(
          "Could not find view.", new IllegalArgumentException(), Response.Status.NOT_FOUND);
    }

    return getSingleVp(visualProperty, view, vps);
  }
Ejemplo n.º 5
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  private final String getViewForVPList(
      final Long networkId,
      final Long viewId,
      final String objectType,
      Collection<VisualProperty<?>> vps) {
    final CyNetworkView networkView = getView(networkId, viewId);
    Collection<? extends View<? extends CyIdentifiable>> graphObjects = null;

    if (objectType.equals("nodes")) {
      graphObjects = networkView.getNodeViews();
    } else if (objectType.equals("edges")) {
      graphObjects = networkView.getEdgeViews();
    } else if (objectType.equals("network")) {
      try {
        return styleSerializer.serializeView(networkView, vps);
      } catch (IOException e) {
        throw getError(
            "Could not serialize the view object.", e, Response.Status.INTERNAL_SERVER_ERROR);
      }
    }

    if (graphObjects == null || graphObjects.isEmpty()) {
      throw getError(
          "Could not find views.", new IllegalArgumentException(), Response.Status.NOT_FOUND);
    }
    try {
      return styleSerializer.serializeViews(graphObjects, vps);
    } catch (IOException e) {
      throw getError(
          "Could not serialize the view object.", e, Response.Status.INTERNAL_SERVER_ERROR);
    }
  }
Ejemplo n.º 6
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  public TaskIterator createTaskIterator(View<CyNode> nView, CyNetworkView netView) {
    List<CyNode> selectedNodes =
        CyTableUtil.getNodesInState(netView.getModel(), CyNetwork.SELECTED, true);
    if (selectedNodes == null || selectedNodes.size() == 0)
      selectedNodes = Collections.singletonList(nView.getModel());

    return new TaskIterator(
        new SMARTSSearchTask(netView.getModel(), selectedNodes, scope, showResult, settings));
  }
Ejemplo n.º 7
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 private final CyNetworkView getView(Long networkId, Long viewId) {
   final Collection<CyNetworkView> views = this.getCyNetworkViews(networkId);
   for (final CyNetworkView view : views) {
     final Long vid = view.getSUID();
     if (vid.equals(viewId)) {
       return view;
     }
   }
   throw new NotFoundException("Could not find view: " + viewId);
 }
Ejemplo n.º 8
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  private void display() {

    CyServiceRegistrarImpl register = new CyServiceRegistrarImpl(bc);

    CyNetworkViewManager viewManager = register.getService(CyNetworkViewManager.class);
    CyNetworkViewFactory viewFactory = register.getService(CyNetworkViewFactory.class);
    CyNetworkView networkView = viewFactory.createNetworkView(network);
    viewManager.addNetworkView(networkView);

    VisualMappingFunctionFactory passthroughFactory =
        register.getService(VisualMappingFunctionFactory.class, "(mapping.type=passthrough)");
    VisualMappingFunctionFactory continuousFactory =
        register.getService(VisualMappingFunctionFactory.class, "(mapping.type=continuous)");
    VisualMappingManager vmManager = register.getService(VisualMappingManager.class);
    VisualStyleFactory vsFactory = register.getService(VisualStyleFactory.class);
    VisualStyle vs =
        vsFactory.createVisualStyle(
            network.getDefaultNetworkTable().getRow(network.getSUID()).get("name", String.class));

    PassthroughMapping pMapping =
        (PassthroughMapping)
            passthroughFactory.createVisualMappingFunction(
                "name", String.class, BasicVisualLexicon.NODE_LABEL);

    vs.addVisualMappingFunction(pMapping);
    vs.apply(networkView);

    ContinuousMapping mapping =
        (ContinuousMapping)
            continuousFactory.createVisualMappingFunction(
                "score", Double.class, BasicVisualLexicon.NODE_FILL_COLOR);

    Double val1 = getMinimum(network.getDefaultNodeTable().getColumn("score"));
    BoundaryRangeValues<Paint> brv1 =
        new BoundaryRangeValues<Paint>(Color.GREEN, Color.GREEN, Color.GREEN);

    Double val3 = getMaximum(network.getDefaultNodeTable().getColumn("score"));
    BoundaryRangeValues<Paint> brv3 =
        new BoundaryRangeValues<Paint>(Color.RED, Color.RED, Color.RED);

    Double val2 = (val1 + val3 + val1 + val1) / 4;
    BoundaryRangeValues<Paint> brv2 =
        new BoundaryRangeValues<Paint>(Color.YELLOW, Color.YELLOW, Color.YELLOW);

    mapping.addPoint(val1, brv1);
    mapping.addPoint(val2, brv2);
    mapping.addPoint(val3, brv3);

    vs.addVisualMappingFunction(mapping);
    vs.apply(networkView);

    vmManager.addVisualStyle(vs);
    vmManager.setVisualStyle(vs, networkView);
    networkView.updateView();
  }
Ejemplo n.º 9
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  private Response getImageForView(String fileType, Long networkId, Long viewId, Integer height) {
    final Collection<CyNetworkView> views = this.getCyNetworkViews(networkId);
    for (final CyNetworkView view : views) {
      final Long vid = view.getSUID();
      if (vid.equals(viewId)) {
        return getImage(fileType, networkId, height);
      }
    }

    throw new NotFoundException("Could not find view for the network: " + networkId);
  }
Ejemplo n.º 10
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 /**
  * @summary Create view for the network
  * @param networkId Network SUID
  * @return SUID for the new Network View.
  */
 @POST
 @Path("/")
 @Produces(MediaType.APPLICATION_JSON)
 public Response createNetworkView(@PathParam("networkId") Long networkId) {
   final CyNetwork network = getCyNetwork(networkId);
   final CyNetworkView view = networkViewFactory.createNetworkView(network);
   networkViewManager.addNetworkView(view);
   return Response.status(Response.Status.CREATED)
       .entity(getNumberObjectString("networkViewSUID", view.getSUID()))
       .build();
 }
Ejemplo n.º 11
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 /**
  * This returns the first view of the network. As of Cytoscape 3.2.x, this is the only view
  * accessible Cytoscape GUI.
  *
  * @summary Convenience method to get the first view model.
  * @param networkId Network SUID
  * @param file (Optional) If you want to get the view as a file, you can specify output file name
  *     with extension. For example, file=test.sif creates new SIF file in the current directory.
  * @return Network view in JSON or location of the file
  */
 @GET
 @Path("/first")
 @Produces(MediaType.APPLICATION_JSON)
 public Response getFirstNetworkView(
     @PathParam("networkId") Long networkId, @QueryParam("file") String file) {
   final Collection<CyNetworkView> views = this.getCyNetworkViews(networkId);
   if (views.isEmpty()) {
     throw new NotFoundException("Could not find view for the network: " + networkId);
   }
   final CyNetworkView view = views.iterator().next();
   return getNetworkView(networkId, view.getSUID(), file);
 }
Ejemplo n.º 12
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  /**
   * @summary Get SUID of all network views
   * @param networkId Network SUID
   * @return Array of all network view SUIDs
   */
  @GET
  @Path("/")
  @Produces(MediaType.APPLICATION_JSON)
  public Collection<Long> getAllNetworkViews(@PathParam("networkId") Long networkId) {
    final Collection<CyNetworkView> views = this.getCyNetworkViews(networkId);

    final Collection<Long> suids = new HashSet<Long>();

    for (final CyNetworkView view : views) {
      final Long viewId = view.getSUID();
      suids.add(viewId);
    }
    return suids;
  }
 private Set<View<CyNode>> getLayoutNodes(CyLayoutAlgorithm layout, CyNetworkView networkView) {
   if (layout.getSupportsSelectedOnly() && selectedTunable.selectedNodesOnly) {
     Set<View<CyNode>> nodeViews = new HashSet<View<CyNode>>();
     CyNetwork network = networkView.getModel();
     for (View<CyNode> view : networkView.getNodeViews()) {
       if (network.getRow(view.getModel()).get(CyNetwork.SELECTED, Boolean.class)
           && view.getVisualProperty(BasicVisualLexicon.NODE_VISIBLE)) {
         nodeViews.add(view);
       }
     }
     return nodeViews;
   }
   return CyLayoutAlgorithm.ALL_NODE_VIEWS;
 }
  void setNetworkView(final CyNetworkView view) {
    getApplyBtn().setEnabled(view != null);

    if (layoutAttrPnl == null) return;

    layoutAttrPnl.removeAll();
    layoutAttrTunable = new LayoutAttributeTunable();

    if (view != null) {
      List<String> attributeList =
          getAttributeList(
              view.getModel(),
              currentLayout.getSupportedNodeAttributeTypes(),
              currentLayout.getSupportedEdgeAttributeTypes());

      if (attributeList.size() > 0) {
        layoutAttrTunable.layoutAttribute = new ListSingleSelection<String>(attributeList);
        layoutAttrTunable.layoutAttribute.setSelectedValue(attributeList.get(0));

        final PanelTaskManager taskMgr = serviceRegistrar.getService(PanelTaskManager.class);
        JPanel panel = taskMgr.getConfiguration(null, layoutAttrTunable);
        setPanelsTransparent(panel);
        layoutAttrPnl.add(panel);
        panel.invalidate();
      }
    }
  }
  private boolean hasSelectedNodes(final CyNetworkView view) {
    if (view == null) return false;

    final CyNetwork network = view.getModel();
    final CyTable table = network.getDefaultNodeTable();

    return table.countMatchingRows(CyNetwork.SELECTED, Boolean.TRUE) > 0;
  }
  public void undo() {
    final Collection<CyNetworkView> views = networkViewManager.getNetworkViews(network);
    CyNetworkView view = null;
    if (views.size() != 0) view = views.iterator().next();

    networkCenterX = view.getVisualProperty(NETWORK_CENTER_X_LOCATION);
    networkCenterY = view.getVisualProperty(NETWORK_CENTER_Y_LOCATION);
    networkCenterZ = view.getVisualProperty(NETWORK_CENTER_Z_LOCATION);
    networkScaleFactor = view.getVisualProperty(NETWORK_SCALE_FACTOR);

    final Collection<View<CyNode>> nodeViews = view.getNodeViews();
    nodesAndLocations = new WeakHashMap<CyNode, NodeLocations>(nodeViews.size());
    for (final View<CyNode> nodeView : nodeViews)
      nodesAndLocations.put(nodeView.getModel(), new NodeLocations(nodeView));

    networkViewManager.destroyNetworkView(view);
  }
  /** 'typical' means that all lines have the form "node1 pd node2 [node3 node4 ...] */
  @Test
  public void testReadFromTypicalFile() throws Exception {
    List<CyNetworkView> views = getViews("sample.sif");

    for (CyNetworkView view : views) {
      for (CyNode n : view.getModel().getNodeList()) {
        System.out.println(
            "sample.sif: NODE " + view.getModel().getRow(n).get("name", String.class));
      }
      for (CyEdge e : view.getModel().getEdgeList()) {
        System.out.println(
            "sample.sif: EDGE " + view.getModel().getRow(e).get("name", String.class));
      }
    }
    CyNetwork net = checkSingleNetwork(views, 31, 27);

    findInteraction(net, "YNL312W", "YPL111W", "pd", 1);
  }
  private void checkNetwork(final CyNetwork network) {
    checkNodeEdgeCount(network, 331, 362, 0, 0);

    // Non-default columns should not be immutable
    assertCy2CustomColumnsAreMutable(network);

    // View test
    Collection<CyNetworkView> views = viewManager.getNetworkViews(network);
    assertEquals(1, views.size());

    final CyNetworkView view = views.iterator().next();
    assertEquals(331, view.getNodeViews().size());
    assertEquals(362, view.getEdgeViews().size());

    // Check updated view
    final VisualStyle style = vmm.getVisualStyle(view);
    style.apply(view);
    checkView(view);
  }
  @Override
  public void run(final TaskMonitor taskMonitor) {
    if (network == null) network = appMgr.getCurrentNetwork();
    Collection<CyNetworkView> views = viewMgr.getNetworkViews(network);

    nodes = nodeList.getValue();

    for (CyNetworkView view : views) {
      Set<View<CyNode>> nodeViews = new HashSet<View<CyNode>>();
      if (nodes == null || nodes.size() == 0) {
        nodeViews = CyLayoutAlgorithm.ALL_NODE_VIEWS;
      } else {
        for (CyNode node : nodes) nodeViews.add(view.getNodeView(node));
      }

      insertTasksAfterCurrentTask(
          algorithm.createTaskIterator(view, layoutContext, nodeViews, getLayoutAttribute()));
    }
  }
  @Override
  public boolean isReady(CyNetworkView networkView) {
    if (!super.isReady(networkView)) return false;

    // Make sure we've got something selected
    List<CyNode> selNodes =
        CyTableUtil.getNodesInState(networkView.getModel(), CyNetwork.SELECTED, true);
    if (selNodes != null && selNodes.size() > 0) return true;

    return false;
  }
Ejemplo n.º 21
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  /**
   * @summary Get view object for the specified type (node or edge)
   * @param networkId Network SUID
   * @param viewId Network view SUID
   * @param objectType nodes or edges
   * @param objectId Object's SUID
   */
  @GET
  @Path("/{viewId}/{objectType}/{objectId}")
  @Produces(MediaType.APPLICATION_JSON)
  public String getView(
      @PathParam("networkId") Long networkId,
      @PathParam("viewId") Long viewId,
      @PathParam("objectType") String objectType,
      @PathParam("objectId") Long objectId) {
    final CyNetworkView networkView = getView(networkId, viewId);

    View<? extends CyIdentifiable> view = null;
    Collection<VisualProperty<?>> lexicon = null;
    if (nodeLexicon == null) {
      initLexicon();
    }

    if (objectType.equals("nodes")) {
      view = networkView.getNodeView(networkView.getModel().getNode(objectId));
      lexicon = nodeLexicon;
    } else if (objectType.equals("edges")) {
      view = networkView.getNodeView(networkView.getModel().getNode(objectId));
      lexicon = edgeLexicon;
    }

    if (view == null) {
      throw getError(
          "Could not find view.", new IllegalArgumentException(), Response.Status.NOT_FOUND);
    }

    try {
      return styleSerializer.serializeView(view, lexicon);
    } catch (IOException e) {
      throw getError(
          "Could not serialize the view object.", e, Response.Status.INTERNAL_SERVER_ERROR);
    }
  }
Ejemplo n.º 22
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  /**
   * By passing list of key-value pair for each Visual Property, update node view.
   *
   * <p>The body should have the following JSON:
   *
   * <pre>
   * [
   * 		{
   * 			"SUID": SUID of node,
   * 			"view": [
   * 				{
   * 					"visualProperty": "Visual Property Name, like NODE_FILL_COLOR",
   * 					"value": "Serialized form of value, like 'red.'"
   * 				},
   * 				...
   * 				{}
   * 			]
   * 		},
   * 		...
   * 		{}
   * ]
   * </pre>
   *
   * Note that this API directly set the value to the view objects, and once Visual Style applied,
   * those values are overridden by the Visual Style.
   *
   * @summary Update node/edge view objects at once
   * @param networkId Network SUID
   * @param viewId Network view SUID
   * @param objectType Type of objects ("nodes" or "edges")
   */
  @PUT
  @Path("/{viewId}/{objectType}")
  @Consumes(MediaType.APPLICATION_JSON)
  public Response updateViews(
      @PathParam("networkId") Long networkId,
      @PathParam("viewId") Long viewId,
      @PathParam("objectType") String objectType,
      final InputStream is) {

    final CyNetworkView networkView = getView(networkId, viewId);

    final ObjectMapper objMapper = new ObjectMapper();

    try {
      // This should be an JSON array.
      final JsonNode rootNode = objMapper.readValue(is, JsonNode.class);

      for (JsonNode entry : rootNode) {
        final Long objectId = entry.get(CyIdentifiable.SUID).asLong();
        final JsonNode viewNode = entry.get("view");
        if (objectId == null || viewNode == null) {
          continue;
        }

        View<? extends CyIdentifiable> view = null;
        if (objectType.equals("nodes")) {
          view = networkView.getNodeView(networkView.getModel().getNode(objectId));
        } else if (objectType.equals("edges")) {
          view = networkView.getEdgeView(networkView.getModel().getEdge(objectId));
        } else if (objectType.equals("network")) {
          view = networkView;
        } else {
          throw getError(
              "Method not supported.",
              new IllegalStateException(),
              Response.Status.INTERNAL_SERVER_ERROR);
        }

        if (view == null) {
          throw getError(
              "Could not find view.", new IllegalArgumentException(), Response.Status.NOT_FOUND);
        }
        styleMapper.updateView(view, viewNode, getLexicon());
      }

      // Repaint
      networkView.updateView();
    } catch (Exception e) {
      throw getError(
          "Could not parse the input JSON for updating view because: " + e.getMessage(),
          e,
          Response.Status.INTERNAL_SERVER_ERROR);
    }
    return Response.ok().build();
  }
Ejemplo n.º 23
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  /**
   * Sets the given AnnotationSet as the "selected" one. If null is passed then all AnnotationSets
   * will be unselected.
   *
   * <p>Note: Currently switching selection is not supported when the currently selected
   * AnnotationSet has collapsed clusters. It is the responsibility of the UI to expand all the
   * clusters before switching the AnnotationSet.
   *
   * <p>MKTODO: It would be better for the model to handle expanding the clusters, but for now we
   * will force the UI to do it.
   *
   * @throws IllegalStateException If the currently active AnnotationSet has collapsed clusters.
   */
  public void select(AnnotationSet annotationSet) {
    if (annotationSet == null || annotationSets.contains(annotationSet)) {

      if (Optional.ofNullable(annotationSet).equals(activeSet)) {
        return;
      }

      if (activeSet.map(AnnotationSet::hasCollapsedCluster).orElse(false)) {
        throw new IllegalStateException("Current AnnotationSet has collapsed clusters");
      }

      CyNetwork network = networkView.getModel();
      activeSet = Optional.ofNullable(annotationSet);

      // ModelManager.handle(AboutToRemoveNodesEvent) only removes nodes from the active annotation
      // set.
      // When switching to a new annotation set we need to "fix" the clusters to remove any nodes
      // that
      // were deleted previously.
      // MKTODO: probably need to test for deleted nodes when serializing the model

      if (annotationSet != null) {
        Set<Cluster> clusters = annotationSet.getClusters();
        for (Cluster cluster :
            new HashSet<>(
                clusters)) { // avoid ConcurrentModificationException because removeNodes() can call
          // delete()
          Set<CyNode> nodesToRemove =
              cluster
                  .getNodes()
                  .stream()
                  .filter(node -> !network.containsNode(node))
                  .collect(Collectors.toSet());

          // Fires ClusterChangedEvent, UI listeners should test if the cluster is part of the
          // active annotation set.
          if (!nodesToRemove.isEmpty()) {
            cluster.removeNodes(nodesToRemove);
          }
        }
      }

      parent.postEvent(new ModelEvents.AnnotationSetSelected(this, activeSet));
    }
  }
Ejemplo n.º 24
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  private final void clearAll(
      final CyNetworkView netView, final View<? extends CyIdentifiable> nodeView) {
    boolean needToUpdateView = false;
    final VisualStyle style = vmm.getCurrentVisualStyle();

    for (VisualProperty<?> vp : vpSet) {
      final boolean lock = nodeView.isDirectlyLocked(vp);
      if (lock) {
        nodeView.clearValueLock(vp);
        needToUpdateView = true;
      }
    }

    if (needToUpdateView) {
      style.apply(netView);
      netView.updateView();
    }
  }
Ejemplo n.º 25
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  /**
   * Apply bypass
   *
   * @param netView
   * @param graphObjectView
   * @param vp
   */
  private final void applBypassValue(
      final CyNetworkView netView,
      final View<? extends CyIdentifiable> graphObjectView,
      VisualProperty<?> vp) {
    final ValueEditor<Object> editor =
        (ValueEditor<Object>) editorManager.getValueEditor(vp.getRange().getType());
    final Object bypassValue = editor.showEditor(null, graphObjectView.getVisualProperty(vp));

    // Set lock for the vp
    graphObjectView.setLockedValue(vp, bypassValue);

    // Apply the new value only for the given view
    // TODO don't do this, because it overwrites some bypassed values with default ones!!! Calling
    // setLockedValue should be enough
    //		final CyRow row = netView.getModel().getRow(graphObjectView.getModel());
    //		vmm.getCurrentVisualStyle().apply(row, graphObjectView);

    // Redraw the view
    netView.updateView();
  }
  public void redo() {
    ;

    final CyNetworkView view = viewFactory.createNetworkView(network);
    networkViewManager.addNetworkView(view);

    for (final View<CyNode> nodeView : view.getNodeViews())
      nodesAndLocations.get(nodeView.getModel()).restoreLocations(nodeView);

    view.setVisualProperty(NETWORK_CENTER_X_LOCATION, networkCenterX);
    view.setVisualProperty(NETWORK_CENTER_Y_LOCATION, networkCenterY);
    view.setVisualProperty(NETWORK_CENTER_Z_LOCATION, networkCenterZ);
    view.setVisualProperty(NETWORK_SCALE_FACTOR, networkScaleFactor);

    eventHelper.flushPayloadEvents();
    view.updateView();
  }
Ejemplo n.º 27
0
 public CyNetwork getNetwork() {
   return networkView.getModel();
 }
Ejemplo n.º 28
0
  @Override
  public List<BarLayer> getLayers(
      CyNetworkView networkView, View<? extends CyIdentifiable> nodeView) {
    CyNetwork network = networkView.getModel();
    if (!(nodeView.getModel() instanceof CyNode)) return null;

    layers = new ArrayList<>();
    CyNode node = (CyNode) nodeView.getModel();

    // Create all of our pie slices. Each slice becomes a layer
    if (attributes != null && attributes.size() > 0) {
      // System.out.println("Getting data from attributes for node "+node);
      values = getDataFromAttributes(network, node, attributes, labels);
      // System.out.println("Data from attributes returns "+values.size()+" values");
      colorList = convertInputToColor(colorString, values);
    }

    // Protect against missing values in the input stream
    // if (values == null || colorList == null) return layers;

    if (labels != null
        && labels.size() > 0
        && (labels.size() != values.size() || labels.size() != colorList.size())) {
      logger.error(
          "barchart: number of labels ("
              + labels.size()
              + "), values ("
              + values.size()
              + "), and colors ("
              + colorList.size()
              + ") don't match");
      return null;
    }

    List<BarLayer> labelList = new ArrayList<BarLayer>();

    double minValue = 0.000001;
    double maxValue = -minValue;
    for (Double val : values) {
      if (val == null) continue;
      minValue = Math.min(minValue, val);
      maxValue = Math.max(maxValue, val);
    }
    double labelMin = minValue;

    if (normalized) {
      minValue = rangeMin;
      maxValue = rangeMax;
    }

    int nBars = values.size();
    Font font = getFont();

    for (int bar = 0; bar < nBars; bar++) {
      String label = null;
      if (labels != null && labels.size() > 0) label = labels.get(bar);
      if (values.get(bar) == null || values.get(bar) == 0.0) continue;

      // System.out.println("Creating bar #"+bar);
      // Create the slice
      BarLayer bl =
          new BarLayer(
              bar,
              nBars,
              separation,
              values.get(bar),
              minValue,
              maxValue,
              normalized,
              ybase,
              colorList.get(bar),
              showAxes,
              borderWidth,
              scale);
      if (bl == null) continue;
      layers.add(bl);
      // System.out.println("BarLayer: "+bar+" bounds: "+bl.getShape().getBounds2D());

      if (label != null) {
        // System.out.println("Creating label for bar #"+bar);
        // Now, create the label
        BarLayer labelLayer =
            new BarLayer(
                bar,
                nBars,
                separation,
                minValue,
                maxValue,
                normalized,
                labelMin,
                ybase,
                label,
                font,
                labelColor,
                showAxes,
                scale);
        if (labelLayer != null) labelList.add(labelLayer);
      }
    }

    // System.out.println("Created "+layers.size()+" bar layers");

    // Now add all of our labels so they will be on top of our slices
    if (labelList != null && labelList.size() > 0) layers.addAll(labelList);

    // System.out.println("Created "+layers.size()+" total layers");

    shapeLayers = layers;
    return layers;
  }
  @Override
  public void run(TaskMonitor taskMonitor) throws Exception {
    desktopApp.getJFrame().getGlassPane().setVisible(true);
    taskMonitor.setTitle("Gene Set / Mutation Analysis");
    taskMonitor.setStatusMessage("Loading file...");
    taskMonitor.setProgress(.25d);
    try {
      Map<String, Integer> geneToSampleNumber = null;
      Map<String, String> geneToSampleString = null;
      Map<String, Set<String>> sampleToGenes = null;
      Set<String> selectedGenes = null;

      if (format.equals("MAF")) {

        sampleToGenes =
            new MATFileLoader().loadSampleToGenes(file.getAbsolutePath(), chooseHomoGenes);
        selectedGenes =
            CancerAnalysisUtilitites.selectGenesInSamples(sampleCutoffValue, sampleToGenes);
      } else if (format.equals("GeneSample")) {
        geneToSampleNumber = new HashMap<String, Integer>();
        geneToSampleString = new HashMap<String, String>();
        loadGeneSampleFile(file, geneToSampleNumber, geneToSampleString);
        selectedGenes = selectGenesBasedOnSampleCutoff(geneToSampleNumber, sampleCutoffValue);
      } else if (format.equals("GeneSet")) {
        selectedGenes = loadGeneSetFile(file);
      }
      // Check if it is possible to construct the network
      // given the sample size.
      if (useLinkers) {
        taskMonitor.setStatusMessage("Checking FI Network size...");
        FINetworkService fiService = PlugInScopeObjectManager.getManager().getNetworkService();
        Integer cutoff = fiService.getNetworkBuildSizeCutoff();
        if (cutoff != null && selectedGenes.size() >= cutoff) {
          JOptionPane.showMessageDialog(
              desktopApp.getJFrame(),
              "The size of the gene set is too big. Linker genes should not be used!\n"
                  + "Please try again without using linker genes.",
              "Error in Building Network",
              JOptionPane.ERROR_MESSAGE);
          desktopApp.getJFrame().getGlassPane().setVisible(false);
          return;
        }
      }

      CytoPanel controlPane = desktopApp.getCytoPanel(CytoPanelName.WEST);
      int selectedIndex = controlPane.getSelectedIndex();
      taskMonitor.setStatusMessage("Constructing FI Network...");
      taskMonitor.setProgress(.50d);
      CyNetwork network = constructFINetwork(selectedGenes, file.getName());
      network.getDefaultNetworkTable().getRow(network.getSUID()).set("name", file.getName());
      if (network == null) {
        JOptionPane.showMessageDialog(
            desktopApp.getJFrame(),
            "Cannot find any functional interaction among provided genes.\n"
                + "No network can be constructed.\n"
                + "Note: only human gene names are supported.",
            "Empty Network",
            JOptionPane.INFORMATION_MESSAGE);
        desktopApp.getJFrame().getGlassPane().setVisible(false);
        return;
      }
      netManager.addNetwork(network);

      // Fix for missing default value persistence in CyTables
      // Should be remedied in the 3.1 api
      CyTable nodeTable = network.getDefaultNodeTable();
      for (Object name : network.getNodeList()) {
        CyNode node = (CyNode) name;
        Long nodeSUID = node.getSUID();
        nodeTable.getRow(nodeSUID).set("isLinker", false);
      }

      controlPane.setSelectedIndex(selectedIndex);
      if (sampleToGenes != null) {
        geneToSampleNumber = new HashMap<String, Integer>();
        geneToSampleString = new HashMap<String, String>();
        Map<String, Set<String>> geneToSamples =
            InteractionUtilities.switchKeyValues(sampleToGenes);
        geneToSamples.keySet().retainAll(selectedGenes);
        for (String gene : geneToSamples.keySet()) {
          Set<String> samples = geneToSamples.get(gene);
          geneToSampleNumber.put(gene, samples.size());
          geneToSampleString.put(gene, InteractionUtilities.joinStringElements(";", samples));
        }
      }
      taskMonitor.setStatusMessage("Formatting network attributes...");
      taskMonitor.setProgress(.65d);
      CyTableManager tableManager = new CyTableManager();
      CyNetworkView view = viewFactory.createNetworkView(network);
      tableManager.storeFINetworkVersion(view);
      tableManager.storeDataSetType(network, CyTableFormatter.getSampleMutationData());
      viewManager.addNetworkView(view);
      if (geneToSampleNumber != null && !geneToSampleNumber.isEmpty()) {
        tableManager.loadNodeAttributesByName(view, "sampleNumber", geneToSampleNumber);
      }
      if (geneToSampleString != null && !geneToSampleString.isEmpty()) {
        tableManager.loadNodeAttributesByName(view, "samples", geneToSampleString);
      }
      // Check if linker genes are to be used.
      if (useLinkers) {
        taskMonitor.setStatusMessage("Fetching linker genes...");
        Map<String, Boolean> geneToIsLinker = new HashMap<String, Boolean>();
        for (Object name : network.getNodeList()) {
          CyNode node = (CyNode) name;
          Long suid = node.getSUID();
          String nodeName = network.getDefaultNodeTable().getRow(suid).get("name", String.class);
          geneToIsLinker.put(nodeName, !selectedGenes.contains(nodeName));
        }
        tableManager.loadNodeAttributesByName(view, "isLinker", geneToIsLinker);
      }
      if (fetchFIAnnotations) {
        taskMonitor.setStatusMessage("Fetching FI annotations...");
        new FIAnnotationHelper().annotateFIs(view, new RESTFulFIService(), tableManager);
      }
      if (view.getModel().getEdgeCount() != 0) {
        for (CyEdge edge : view.getModel().getEdgeList()) {
          tableManager.storeEdgeName(edge, view);
        }
      }
      BundleContext context = PlugInScopeObjectManager.getManager().getBundleContext();
      ServiceReference visHelperRef = context.getServiceReference(FIVisualStyle.class.getName());
      if (visHelperRef != null) {
        FIVisualStyleImpl styleHelper = (FIVisualStyleImpl) context.getService(visHelperRef);
        styleHelper.setVisualStyle(view);
        styleHelper.setLayout();
      }
      //            BundleContext context =
      // PlugInScopeObjectManager.getManager().getBundleContext();
      //            ServiceReference styleHelperRef =
      // context.getServiceReference(FIVisualStyleImpl.class.getName());
      //            FIVisualStyleImpl styleHelper = (FIVisualStyleImpl)
      // context.getService(styleHelperRef);

      taskMonitor.setProgress(1.0d);
    } catch (Exception e) {
      JOptionPane.showMessageDialog(
          desktopApp.getJFrame(),
          "Error in Loading File: " + e.getMessage(),
          "Error in Loading",
          JOptionPane.ERROR_MESSAGE);
      desktopApp.getJFrame().getGlassPane().setVisible(false);
    }
    desktopApp.getJFrame().getGlassPane().setVisible(false);
  }
  @Override
  public void serialize(CyNetworkView networkView, JsonGenerator jgen, SerializerProvider provider)
      throws IOException, JsonProcessingException {
    jgen.useDefaultPrettyPrinter();

    jgen.writeStartObject();
    jgen.writeStringField(
        CytoscapeJsNetworkModule.FORMAT_VERSION_TAG, CytoscapeJsNetworkModule.FORMAT_VERSION);
    jgen.writeStringField(CytoscapeJsNetworkModule.GENERATED_BY_TAG, "cytoscape-" + version);
    jgen.writeStringField(
        CytoscapeJsNetworkModule.TARGET_CYJS_VERSION_TAG,
        CytoscapeJsNetworkModule.CYTOSCAPEJS_VERSION);

    final CyNetwork network = networkView.getModel();

    // Serialize network data table
    jgen.writeObjectFieldStart(DATA.getTag());
    jgen.writeObject(network.getRow(network));
    jgen.writeEndObject();

    jgen.writeObjectFieldStart(ELEMENTS.getTag());

    // Write array
    final List<CyNode> nodes = network.getNodeList();
    final List<CyEdge> edges = network.getEdgeList();

    jgen.writeArrayFieldStart(NODES.getTag());
    for (final CyNode node : nodes) {
      jgen.writeStartObject();

      // Data field
      jgen.writeObjectFieldStart(DATA.getTag());
      jgen.writeStringField(ID.getTag(), node.getSUID().toString());
      // Write CyRow in "data" field
      jgen.writeObject(network.getRow(node));
      jgen.writeEndObject();

      // Position and other visual props
      jgen.writeObject(networkView.getNodeView(node));

      // Special case for cytoscape.js format:
      // - Selected
      jgen.writeBooleanField(
          CyNetwork.SELECTED, network.getRow(node).get(CyNetwork.SELECTED, Boolean.class));

      jgen.writeEndObject();
    }
    jgen.writeEndArray();

    jgen.writeArrayFieldStart(EDGES.getTag());
    for (final CyEdge edge : edges) {
      jgen.writeStartObject();

      jgen.writeObjectFieldStart(DATA.getTag());
      jgen.writeStringField(ID.getTag(), edge.getSUID().toString());
      jgen.writeStringField(SOURCE.getTag(), edge.getSource().getSUID().toString());
      jgen.writeStringField(TARGET.getTag(), edge.getTarget().getSUID().toString());

      // Write CyRow in "data" field
      jgen.writeObject(network.getRow(edge));

      jgen.writeEndObject();

      // Special case for cytoscape.js format:
      // - Selected
      jgen.writeBooleanField(
          CyNetwork.SELECTED, network.getRow(edge).get(CyNetwork.SELECTED, Boolean.class));

      jgen.writeEndObject();
    }
    jgen.writeEndArray();

    jgen.writeEndObject();
  }