Examples with InfoFile edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.TransClust.de.layclust.taskmanaging.io.InfoFile used on opensource projects

Example 1 with InfoFile

use of edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.TransClust.de.layclust.taskmanaging.io.InfoFile 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 */
}