Examples with IteratorThread edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.TransClust.de.layclust.iterativeclustering.IteratorThread used on opensource projects

Example 1 with IteratorThread

use of edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.TransClust.de.layclust.iterativeclustering.IteratorThread in project clusterMaker2 by RBVI.

the class RunTransClust method run.

public List<NodeCluster> run(TaskMonitor monitor, CyNetwork network) {
    DoubleMatrix2D matrix = this.distanceMatrix.getColtMatrix();
    nodes = distanceMatrix.getRowNodes();
    HashMap<String, CyNode> nodeHash = new HashMap<String, CyNode>();
    for (CyNode node : nodes) {
        nodeHash.put(ModelUtils.getNodeName(network, node), node);
    }
    HashMap<String, Integer> integers2proteins = new HashMap<String, Integer>();
    HashMap<Integer, String> proteins2integers = new HashMap<Integer, String>();
    int count = 0;
    for (CyNode node : this.nodes) {
        integers2proteins.put(ModelUtils.getNodeName(network, node), count);
        proteins2integers.put(count, ModelUtils.getNodeName(network, node));
        count++;
    }
    Edges es = new Edges(this.nodes.size() * this.nodes.size(), this.nodes.size());
    count = 0;
    for (int i = 0; i < this.nodes.size(); i++) {
        CyNode cyNodeI = this.nodes.get(i);
        es.startPositions[integers2proteins.get(cyNodeI.getSUID())] = count;
        for (int j = 0; j < this.nodes.size(); j++) {
            CyNode cyNodeJ = this.nodes.get(j);
            es.sources[count] = i;
            es.targets[count] = j;
            Double val = distanceMatrix.getValue(i, j);
            if (val != null) {
                es.values[count] = val.floatValue();
                count++;
            }
        }
        es.endPositions[integers2proteins.get(cyNodeI.getSUID())] = count - 1;
    }
    Semaphore s = new Semaphore(1);
    TaskConfig.mode = TaskConfig.COMPARISON_MODE;
    TaskConfig.monitor = monitor;
    IteratorThread it = new IteratorThread(es, integers2proteins, proteins2integers, s);
    TaskConfig.minThreshold = threshold;
    TaskConfig.maxThreshold = threshold;
    try {
        s.acquire();
    } catch (InterruptedException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
    it.start();
    monitor.showMessage(TaskMonitor.Level.INFO, "Executing TransClust Clustering...");
    try {
        s.acquire();
    } catch (InterruptedException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
    monitor.showMessage(TaskMonitor.Level.INFO, "Assigning nodes to clusters");
    String result = it.resultsStringBuffer.toString();
    String[] clusters = result.split("\t")[2].split(";");
    Map<Integer, NodeCluster> clusterMap = getClusterMap(clusters, nodeHash);
    // Update node attributes in network to include clusters. Create cygroups from clustered nodes
    monitor.showMessage(TaskMonitor.Level.INFO, "Created " + clusterMap.size() + " clusters");
    if (clusterCount == 0) {
        monitor.showMessage(TaskMonitor.Level.ERROR, "Created 0 clusters!!!!");
        return null;
    }
    int clusterNumber = 1;
    Map<NodeCluster, NodeCluster> cMap = new HashMap();
    for (NodeCluster cluster : NodeCluster.sortMap(clusterMap)) {
        if (cMap.containsKey(cluster))
            continue;
        cMap.put(cluster, cluster);
        cluster.setClusterNumber(clusterNumber);
        clusterNumber++;
    }
    Set<NodeCluster> clusters2 = cMap.keySet();
    return new ArrayList<NodeCluster>(clusters2);
}

Example 2 with IteratorThread

use of edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.TransClust.de.layclust.iterativeclustering.IteratorThread in project clusterMaker2 by RBVI.

the class ClusteringManagerTask method run.

public void run() {
    try {
        TaskConfig.monitor.setStatusMessage("-----------------------------------");
        TaskConfig.monitor.setStatusMessage("Running ... " + TaskConfig.NAME + " v" + TaskConfig.VERSION);
        Date date = new Date(System.currentTimeMillis());
        TaskConfig.monitor.setStatusMessage(date.toString());
        TaskConfig.monitor.setStatusMessage("-----------------------------------");
        if (TaskConfig.mode == TaskConfig.CLUSTERING_MODE) {
            long time = System.currentTimeMillis();
            this.clusterManager = new ClusteringManager(TaskConfig.cmPath);
            try {
                this.clusterManager.initParametersAndCCs();
                this.clusterManager.runClustering();
                // System.out.println(this.clusterManager.getConnectedComponents().size());
                time = System.currentTimeMillis() - time;
                TaskConfig.monitor.setStatusMessage("Time taken for complete clustering process: " + TaskUtility.convertTime(time));
            } catch (InvalidInputFileException e) {
                TaskConfig.monitor.showMessage(TaskMonitor.Level.ERROR, e.getMessage());
                // e.printStackTrace();
                System.exit(-1);
            } catch (InvalidTypeException e) {
                TaskConfig.monitor.showMessage(TaskMonitor.Level.ERROR, e.getMessage());
                // e.printStackTrace();
                System.exit(-1);
            }
        } else /* start general training */
        if (TaskConfig.mode == TaskConfig.GENERAL_TRAINING_MODE) {
            try {
                long time = System.currentTimeMillis();
                ClusteringManager clustermanage = new ClusteringManager(TaskConfig.cmPath);
                GeneralParameterTraining generalParameterTraining = new GeneralParameterTraining(clustermanage);
                IParameters[] layoutParams = generalParameterTraining.runGeneralTraining();
                /* save newly found parameters to config file */
                TaskConfig.saveConfigurationsToConfigFile(TaskConfig.outConfigPath);
                /* print out information about training */
                TaskConfig.monitor.setStatusMessage(TaskConfig.NL + "###### Best Parameter Configurations Found ######");
                for (int i = 0; i < layoutParams.length; i++) {
                    TaskConfig.monitor.setStatusMessage(layoutParams[i].toString());
                    InfoFile.appendLnProjectResults(layoutParams[i].toString());
                }
                time = System.currentTimeMillis() - time;
                TaskConfig.monitor.setStatusMessage("Time taken for complete general training: " + TaskUtility.convertTime(time));
            } catch (InvalidInputFileException e) {
                TaskConfig.monitor.showMessage(TaskMonitor.Level.ERROR, e.getMessage());
            // e.printStackTrace();
            } catch (InvalidTypeException e) {
                TaskConfig.monitor.showMessage(TaskMonitor.Level.ERROR, e.getMessage());
            // e.printStackTrace();
            }
        } else if (TaskConfig.mode == TaskConfig.COMPARISON_MODE || TaskConfig.mode == TaskConfig.HIERARICHAL_MODE) {
            Thread t = new IteratorThread();
            t.start();
        } else /* no such mode */
        {
            TaskConfig.monitor.showMessage(TaskMonitor.Level.ERROR, "ERROR: This mode does not exist: " + TaskConfig.mode);
        }
        /* create info file */
        if (TaskConfig.info) {
            InfoFile info = new InfoFile();
            info.instantiateFile(TaskConfig.infoPath);
            info.createAndCloseInfoFile();
            /* clear information from StringBuffers in InfoFile */
            InfoFile.clearData();
        }
    // /* ====== CLEAN UP AT END ====== */
    } catch (Exception e) {
        TaskConfig.monitor.showMessage(TaskMonitor.Level.ERROR, "ERROR occured in run with the following message: " + e.getMessage());
    // e.printStackTrace();
    }
    /* release permit in semaphore if necessary */
    if (semaphore != null) {
        semaphore.release();
    }
/* reset the run button back to "RUN" and reset action command */
}