Examples with CyEdge org.cytoscape.model.CyEdge used on opensource projects

Example 26 with CyEdge

use of org.cytoscape.model.CyEdge in project cytoscape-impl by cytoscape.

the class CopyExistingViewTask method run.

@Override
public void run(TaskMonitor tm) {
    if (sourceView == null)
        throw new NullPointerException("source network view is null.");
    if (newView == null)
        throw new NullPointerException("new network view is null.");
    tm.setProgress(0.0);
    final Collection<RenderingEngine<?>> engines = renderingEngineMgr.getAllRenderingEngines();
    Collection<VisualProperty<?>> nodeProps = null;
    Collection<VisualProperty<?>> edgeProps = null;
    if (!engines.isEmpty()) {
        final VisualLexicon lexicon = engines.iterator().next().getVisualLexicon();
        nodeProps = lexicon.getAllDescendants(BasicVisualLexicon.NODE);
        edgeProps = lexicon.getAllDescendants(BasicVisualLexicon.EDGE);
    }
    // Copy some network view properties
    if (!fitContent) {
        newView.setVisualProperty(BasicVisualLexicon.NETWORK_CENTER_X_LOCATION, sourceView.getVisualProperty(BasicVisualLexicon.NETWORK_CENTER_X_LOCATION));
        newView.setVisualProperty(BasicVisualLexicon.NETWORK_CENTER_Y_LOCATION, sourceView.getVisualProperty(BasicVisualLexicon.NETWORK_CENTER_Y_LOCATION));
        newView.setVisualProperty(BasicVisualLexicon.NETWORK_CENTER_Z_LOCATION, sourceView.getVisualProperty(BasicVisualLexicon.NETWORK_CENTER_Z_LOCATION));
        newView.setVisualProperty(BasicVisualLexicon.NETWORK_SCALE_FACTOR, sourceView.getVisualProperty(BasicVisualLexicon.NETWORK_SCALE_FACTOR));
        newView.setVisualProperty(BasicVisualLexicon.NETWORK_WIDTH, sourceView.getVisualProperty(BasicVisualLexicon.NETWORK_WIDTH));
        newView.setVisualProperty(BasicVisualLexicon.NETWORK_HEIGHT, sourceView.getVisualProperty(BasicVisualLexicon.NETWORK_HEIGHT));
        newView.setVisualProperty(BasicVisualLexicon.NETWORK_DEPTH, sourceView.getVisualProperty(BasicVisualLexicon.NETWORK_DEPTH));
    }
    // Copy node locations and locked visual properties
    for (final View<CyNode> newNodeView : newView.getNodeViews()) {
        final View<CyNode> origNodeView = getOriginalNodeView(newNodeView);
        if (origNodeView == null)
            continue;
        newNodeView.setVisualProperty(BasicVisualLexicon.NODE_X_LOCATION, origNodeView.getVisualProperty(BasicVisualLexicon.NODE_X_LOCATION));
        newNodeView.setVisualProperty(BasicVisualLexicon.NODE_Y_LOCATION, origNodeView.getVisualProperty(BasicVisualLexicon.NODE_Y_LOCATION));
        if (nodeProps != null) {
            // Set lock (if necessary)
            for (final VisualProperty vp : nodeProps) {
                if (origNodeView.isValueLocked(vp))
                    newNodeView.setLockedValue(vp, origNodeView.getVisualProperty(vp));
            }
        }
    }
    tm.setProgress(0.5);
    // Copy edge locked visual properties
    for (final View<CyEdge> newEdgeView : newView.getEdgeViews()) {
        final View<CyEdge> origEdgeView = getOriginalEdgeView(newEdgeView);
        if (origEdgeView != null && edgeProps != null) {
            // Set lock (if necessary)
            for (final VisualProperty vp : edgeProps) {
                if (origEdgeView.isValueLocked(vp))
                    newEdgeView.setLockedValue(vp, origEdgeView.getVisualProperty(vp));
            }
        }
    }
    tm.setProgress(0.9);
    if (style != null) {
        style.apply(newView);
        newView.updateView();
    }
    if (fitContent)
        newView.fitContent();
    tm.setProgress(1.0);
}

Example 27 with CyEdge

use of org.cytoscape.model.CyEdge in project cytoscape-impl by cytoscape.

the class SelectAdjacentEdgesTaskTest method testRun.

@Test
public void testRun() throws Exception {
    UndoSupport undoSupport = mock(UndoSupport.class);
    when(r3.get("selected", Boolean.class)).thenReturn(true);
    when(r4.get("selected", Boolean.class)).thenReturn(false);
    Set<Long> selectedNodes = new HashSet<>();
    selectedNodes.add(r3.get(CyNetwork.SUID, Long.class));
    when(nodeTable.getMatchingKeys(CyNetwork.SELECTED, true, Long.class)).thenReturn(selectedNodes);
    List<CyEdge> el = new ArrayList<CyEdge>();
    el.add(e1);
    when(net.getAdjacentEdgeList(e3, CyEdge.Type.ANY)).thenReturn(el);
    // run the task
    Task t = new SelectAdjacentEdgesTask(undoSupport, net, networkViewManager, eventHelper);
    t.run(tm);
    // check that the expected rows were set
    verify(r1, times(1)).set("selected", true);
}

Example 28 with CyEdge

use of org.cytoscape.model.CyEdge in project cytoscape-impl by cytoscape.

the class NumericFilter method apply.

public void apply() {
    List<CyNode> nodes_list = null;
    List<CyEdge> edges_list = null;
    int objectCount = -1;
    if (index_type == QuickFind.INDEX_NODES) {
        nodes_list = network.getNodeList();
        objectCount = nodes_list.size();
        // all the bits are false initially
        node_bits = new BitSet(objectCount);
    } else if (index_type == QuickFind.INDEX_EDGES) {
        edges_list = network.getEdgeList();
        objectCount = edges_list.size();
        // all the bits are false initially
        edge_bits = new BitSet(objectCount);
    } else {
        LoggerFactory.getLogger("org.cytoscape.application.userlog").error("StringFilter: Index_type is undefined.");
        return;
    }
    if (lowBound == null || highBound == null || network == null || !FilterUtil.hasSuchAttribute(network, controllingAttribute, index_type)) {
        return;
    }
    // If quickFind_index does not exist, build the Index
    // if (quickFind_index == null) {
    quickFind_index = FilterUtil.getQuickFindIndex(quickFind, controllingAttribute, network, index_type);
    // }
    // System.out.println(" NumberFilter.apply(): objectCount = " + objectCount);
    NumberIndex numberIndex = (NumberIndex) quickFind_index;
    List<?> list = numberIndex.getRange(lowBound, highBound);
    if (list.size() == 0) {
        return;
    }
    int index;
    if (index_type == QuickFind.INDEX_NODES) {
        for (Object obj : list) {
            index = nodes_list.lastIndexOf(obj);
            node_bits.set(index, true);
        }
    } else if (index_type == QuickFind.INDEX_EDGES) {
        for (Object obj : list) {
            index = edges_list.lastIndexOf(obj);
            edge_bits.set(index, true);
        }
    }
    if (negation) {
        if (index_type == QuickFind.INDEX_NODES) {
            node_bits.flip(0, objectCount);
        }
        if (index_type == QuickFind.INDEX_EDGES) {
            edge_bits.flip(0, objectCount);
        }
    }
}

Example 29 with CyEdge

use of org.cytoscape.model.CyEdge in project cytoscape-impl by cytoscape.

the class StringFilter method apply.

/**
 * Caculate the bitSet based on the existing TextIndex and search string.
 * The size of the bitSet is the number of nodes/edges in the given network,
 * All bits are initially set to false, those with hits are set to true.
 * @param none.
 * @return none.
 */
public void apply() {
    List<CyNode> nodes_list = null;
    List<CyEdge> edges_list = null;
    // Initialize the bitset
    int objectCount = -1;
    if (index_type == QuickFind.INDEX_NODES) {
        nodes_list = network.getNodeList();
        objectCount = nodes_list.size();
        // all the bits are false at very beginning
        node_bits = new BitSet(objectCount);
    } else if (index_type == QuickFind.INDEX_EDGES) {
        edges_list = network.getEdgeList();
        objectCount = edges_list.size();
        // all the bits are false at very beginning
        edge_bits = new BitSet(objectCount);
    } else {
        LoggerFactory.getLogger("org.cytoscape.application.userlog").error("StringFilter: Index_type is undefined.");
        return;
    }
    if (searchStr == null || network == null || !FilterUtil.hasSuchAttribute(network, controllingAttribute, index_type)) {
        return;
    }
    // If quickFind_index does not exist, build the Index
    // if (quickFind_index == null) {
    quickFind_index = FilterUtil.getQuickFindIndex(quickFind, controllingAttribute, network, index_type);
    // }
    TextIndex theIndex = (TextIndex) quickFind_index;
    Hit[] hits = theIndex.getHits(searchStr, Integer.MAX_VALUE);
    if (hits.length == 0) {
        return;
    }
    Hit hit0 = hits[0];
    Object[] hit_objs = hit0.getAssociatedObjects();
    int index = -1;
    if (index_type == QuickFind.INDEX_NODES) {
        for (Object obj : hit_objs) {
            index = nodes_list.indexOf(obj);
            node_bits.set(index, true);
        }
    } else if (index_type == QuickFind.INDEX_EDGES) {
        for (Object obj : hit_objs) {
            index = edges_list.indexOf(obj);
            edge_bits.set(index, true);
        }
    }
    if (negation) {
        if (index_type == QuickFind.INDEX_NODES) {
            node_bits.flip(0, objectCount);
        }
        if (index_type == QuickFind.INDEX_EDGES) {
            edge_bits.flip(0, objectCount);
        }
    }
}

Example 30 with CyEdge

use of org.cytoscape.model.CyEdge in project cytoscape-impl by cytoscape.

the class ApplyFilterThread method passAtomicFilter.

private boolean passAtomicFilter(CyNetwork network, Object pObject, AtomicFilter pAtomicFilter) {
    CyRow data = null;
    if (pObject instanceof CyNode) {
        CyNode node = (CyNode) pObject;
        data = network.getRow(node);
    } else {
        CyEdge edge = (CyEdge) pObject;
        data = network.getRow(edge);
    }
    if (pAtomicFilter instanceof StringFilter) {
        StringFilter theStringFilter = (StringFilter) pAtomicFilter;
        String value = data.get(theStringFilter.getControllingAttribute().substring(5), String.class);
        if (value == null) {
            return false;
        }
        if (theStringFilter == null) {
            return false;
        }
        if (theStringFilter.getSearchStr() == null) {
            return false;
        }
        String[] pattern = theStringFilter.getSearchStr().split("\\s");
        for (int p = 0; p < pattern.length; ++p) {
            if (!Strings.isLike(value, pattern[p], 0, true)) {
                // this is an OR function
                return false;
            }
        }
    } else if (pAtomicFilter instanceof NumericFilter) {
        NumericFilter theNumericFilter = (NumericFilter) pAtomicFilter;
        Number value;
        if (data.getTable().getColumn(theNumericFilter.getControllingAttribute().substring(5)).getType() == Double.class)
            value = data.get(theNumericFilter.getControllingAttribute().substring(5), Double.class);
        else
            value = data.get(theNumericFilter.getControllingAttribute().substring(5), Integer.class);
        if (value == null) {
            return false;
        }
        Double lowValue = (Double) theNumericFilter.getLowBound();
        Double highValue = (Double) theNumericFilter.getHighBound();
        // To correct the boundary values for lowValue and highValue
        if (lowValue.doubleValue() > 0.0) {
            lowValue = lowValue * 0.99999;
        } else {
            lowValue = lowValue * 1.00001;
        }
        if (highValue.doubleValue() > 0.0) {
            highValue = highValue * 1.00001;
        } else {
            highValue = highValue * 0.99999;
        }
        // if (!(value.doubleValue() >= lowValue.doubleValue() && value.doubleValue()<= highValue.doubleValue())) {
        if (!((Double.compare(value.doubleValue(), lowValue.doubleValue()) >= 0) && (Double.compare(value.doubleValue(), highValue.doubleValue())) <= 0)) {
            return false;
        }
    }
    return true;
}