Examples with MCODEParameters ca.utoronto.tdccbr.mcode.internal.model.MCODEParameters used on opensource projects

Example 1 with MCODEParameters

use of ca.utoronto.tdccbr.mcode.internal.model.MCODEParameters in project MCODE by BaderLab.

the class AnalysisAction method execute.

private void execute(CyNetwork network, TaskObserver taskObserver) {
    int resultId = resultsMgr.getNextResultId();
    var currentParams = mcodeUtil.getParameterManager().getLiveParams().copy();
    var nodes = network.getNodeList();
    var selectedNodes = new ArrayList<Long>();
    for (CyNode n : nodes) {
        if (network.getRow(n).get(CyNetwork.SELECTED, Boolean.class))
            selectedNodes.add(n.getSUID());
    }
    var selectedNodesRGI = selectedNodes.toArray(new Long[selectedNodes.size()]);
    currentParams.setSelectedNodes(selectedNodesRGI);
    final MCODEAlgorithm alg;
    MCODEParameters savedParams = null;
    // otherwise we construct a new alg class
    if (mcodeUtil.containsNetworkAlgorithm(network.getSUID())) {
        alg = mcodeUtil.getNetworkAlgorithm(network.getSUID());
        // Get a copy of the last saved parameters for comparison with the current ones
        savedParams = mcodeUtil.getParameterManager().getNetworkParams(network.getSUID());
    } else {
        alg = new MCODEAlgorithm(null, mcodeUtil);
        mcodeUtil.addNetworkAlgorithm(network.getSUID(), alg);
        mode = FIRST_TIME;
    }
    var interruptedMessage = "";
    // the clustering parameters are relevant if the optimization is used
    if (mode == FIRST_TIME || isDirty(network) || (savedParams != null && (currentParams.getIncludeLoops() != savedParams.getIncludeLoops() || currentParams.getDegreeCutoff() != savedParams.getDegreeCutoff()))) {
        mode = RESCORE;
        logger.debug("Analysis: score network, find clusters");
        mcodeUtil.getParameterManager().setParams(currentParams, resultId, network);
    } else {
        var res = resultsMgr.getFreshResult(network.getSUID(), currentParams);
        if (res != null) {
            mode = INTERRUPTION;
            interruptedMessage = "The parameters you specified have not changed\n" + "(you used the same parameters in analysis #" + res.getId() + ").";
        } else {
            mode = REFIND;
            logger.debug("Analysis: find clusters");
            mcodeUtil.getParameterManager().setParams(currentParams, resultId, network);
        }
    }
    // In case the user selected selection scope we must make sure that they selected at least 1 node
    if (currentParams.getScope() == MCODEAnalysisScope.SELECTION && currentParams.getSelectedNodes().length < 1) {
        mode = INTERRUPTION;
        interruptedMessage = "You must first SELECT one or more NODES for this scope.";
    }
    if (mode == INTERRUPTION) {
        JOptionPane.showMessageDialog(swingApplication.getJFrame(), interruptedMessage, "Analysis Interrupted", JOptionPane.WARNING_MESSAGE);
    } else {
        // Run MCODE
        var tf = new MCODEAnalyzeTaskFactory(network, mode, resultId, alg, resultsMgr, mcodeUtil);
        registrar.getService(DialogTaskManager.class).execute(tf.createTaskIterator(), taskObserver);
    }
}

Example 2 with MCODEParameters

use of ca.utoronto.tdccbr.mcode.internal.model.MCODEParameters in project MCODE by BaderLab.

the class MCODEAlgorithmTest method testCompleteGraphIncludingLoops.

@Test
public void testCompleteGraphIncludingLoops() {
    CyNetwork net = createCompleteGraph(16);
    int resultId = resultsMgr.getNextResultId();
    MCODEParameters params = new MCODEParameters();
    params.setIncludeLoops(true);
    List<MCODECluster> clusters = findClusters(net, params);
    assertEquals(1, clusters.size());
    MCODECluster c = clusters.get(0);
    CySubNetwork cn = c.getNetwork();
    assertNotNull(cn);
    assertEquals(resultId, c.getResultId());
    assertEquals(14.118, c.getScore(), 0.0009);
    assertEquals(16, cn.getNodeCount());
    assertEquals(120, cn.getEdgeCount());
    assertNotNull(c.getSeedNode());
// TODO: fix
// check scores of all nodes
// for (CyNode n : cn.getNodeList()) {
// assertEquals(13.345, alg.getNodeScore(n.getSUID(), resultId), 0.001);
// }
}

Example 3 with MCODEParameters

use of ca.utoronto.tdccbr.mcode.internal.model.MCODEParameters in project MCODE by BaderLab.

the class MCODEUtilTest method testDisposeUnnusedNetworks.

@Test
public void testDisposeUnnusedNetworks() {
    final CyNetwork net = createCompleteGraph(16);
    final CyRootNetwork rn = netViewTestSupport.getRootNetworkFactory().getRootNetwork(net);
    int originalNetCount = rn.getSubNetworkList().size();
    final List<MCODECluster> clusters = findClusters(net);
    assertEquals(1, clusters.size());
    MCODEResult res = resultsMgr.createResult(net, new MCODEParameters(), clusters);
    mcodeUtil.disposeUnusedNetworks(Collections.singleton(res));
    assertEquals(originalNetCount + clusters.size(), rn.getSubNetworkList().size());
}