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

Example 56 with CyEdge

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

the class SimpleNetwork method removeEdgesInternal.

protected boolean removeEdgesInternal(final Collection<CyEdge> edges) {
    if (edges == null || edges.isEmpty())
        return false;
    boolean madeChanges = false;
    synchronized (lock) {
        for (CyEdge edge : edges) {
            if (!containsEdge(edge))
                continue;
            final EdgePointer e = (EdgePointer) edgePointers.get(edge.getSUID());
            edgePointers.removeKey(edge.getSUID());
            e.remove();
            edgeCount--;
            madeChanges = true;
        }
    }
    return madeChanges;
}

Example 57 with CyEdge

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

the class SimpleNetwork method getEdgeList.

public List<CyEdge> getEdgeList() {
    synchronized (lock) {
        final List<CyEdge> ret = new ArrayList<>(edgeCount);
        EdgePointer edge = null;
        int numRemaining = edgeCount;
        NodePointer node = firstNode;
        while (numRemaining > 0) {
            final CyEdge retEdge;
            if (edge != null) {
                retEdge = edge.cyEdge;
            } else {
                for (edge = node.firstOutEdge; edge == null; node = node.nextNode, edge = node.firstOutEdge) ;
                node = node.nextNode;
                retEdge = edge.cyEdge;
            }
            edge = edge.nextOutEdge;
            numRemaining--;
            ret.add(retEdge);
        }
        return ret;
    }
}

Example 58 with CyEdge

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

the class ScaleLayouter method scaleGraph.

/**
 * A scaleFactor of 1.0 does not move anything.
 *
 * @exception IllegalArgumentException if
 *   scaleFactor < 0.001 or if scaleFactor > 1000.0.
 */
public void scaleGraph(double scaleFactor, final Direction direction) {
    if ((scaleFactor < 0.001d) || (scaleFactor > 1000.0d))
        throw new IllegalArgumentException("scaleFactor is outside allowable range [0.001, 1000.0]");
    if (m_translationToOrig == null)
        return;
    double xFactor = scaleFactor, yFactor = scaleFactor;
    switch(direction) {
        case X_AXIS_ONLY:
            yFactor = 1.0;
            break;
        case Y_AXIS_ONLY:
            xFactor = 1.0;
            break;
        case BOTH_AXES:
            /* Intentionally empty. */
            break;
    }
    final AffineTransform3D xform = m_translationToOrig.concatenatePost((new Scale3D(xFactor, yFactor, 1.0d)).concatenatePost(m_translationFromOrig));
    for (CyNode node : m_graph.nodes()) {
        if (!m_graph.isMovableNode(node))
            continue;
        m_pointBuff[0] = m_graph.getNodePosition(node, true);
        m_pointBuff[1] = m_graph.getNodePosition(node, false);
        m_pointBuff[2] = 0.0d;
        xform.transformArr(m_pointBuff);
        m_graph.setNodePosition(node, m_pointBuff[0], m_pointBuff[1]);
    }
    for (CyEdge edge : m_graph.edges()) {
        if (!(m_graph.isMovableNode(edge.getSource())) && m_graph.isMovableNode(edge.getTarget()))
            continue;
    /* TODO support anchors
			final int numAnchors = m_graph.getNumAnchors(edge);

			for (int j = 0; j < numAnchors; j++) {
				m_pointBuff[0] = m_graph.getAnchorPosition(edge, j, true);
				m_pointBuff[1] = m_graph.getAnchorPosition(edge, j, false);
				m_pointBuff[2] = 0.0d;
				xform.transformArr(m_pointBuff);
				m_graph.setAnchorPosition(edge, j, m_pointBuff[0], m_pointBuff[1]);
			}
			*/
    }
}

Example 59 with CyEdge

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

the class CyRootNetworkImpl method addEdge.

@Override
public CyEdge addEdge(final CyNode s, final CyNode t, final boolean directed) {
    final CyEdge edge;
    synchronized (lock) {
        edge = new CyEdgeImpl(SUIDFactory.getNextSUID(), s, t, directed, getNextEdgeIndex());
        addEdgeInternal(s, t, directed, edge);
    }
    return edge;
}

Example 60 with CyEdge

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

the class CySubNetworkImpl method copyTableData.

/**
 * This method is called when an edge or a node is added to the networks
 * which is indeed a copy of another edge/node. Hence, it copies all of the
 * default attributes from the shared table referenced to that edge/node to
 * the new edge/node.
 * @param graphObject
 */
private void copyTableData(final CyIdentifiable graphObject) {
    final String name = parent.getRow(graphObject).get(NAME, String.class);
    final CyRow sharedTableRow = parent.getRow(graphObject, CyRootNetwork.SHARED_ATTRS);
    final CyRow defaultTableRow = parent.getRow(graphObject);
    // final String name = parent.getCachedAttributes(graphObject).get(NAME, String.class);
    // final CyRow sharedTableRow = parent.getCachedAttributes(graphObject, CyRootNetwork.SHARED_ATTRS);
    // final CyRow defaultTableRow = parent.getCachedAttributes(graphObject);
    final CyRow targetRow = this.getRow(graphObject);
    // Step 1: Copy shared name as name of this new node
    final String sharedName = sharedTableRow.get(CyRootNetwork.SHARED_NAME, String.class);
    if (sharedName != null)
        targetRow.set(CyNetwork.NAME, sharedName);
    else
        targetRow.set(CyNetwork.NAME, name);
    // Step 2: Copy selection state
    targetRow.set(CyNetwork.SELECTED, defaultTableRow.get(CyNetwork.SELECTED, Boolean.class));
    // Step 3: Copy Interaction if edge
    if (graphObject instanceof CyEdge) {
        final String interaction = sharedTableRow.get(CyRootNetwork.SHARED_INTERACTION, String.class);
        targetRow.set(CyEdge.INTERACTION, interaction);
    }
}