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

Example 1 with ClusteringManagerTask

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

the class Console method parseArgsAndInitProgram.

/**
 * This method parses the input parameters from the console and starts the
 * program with the correct parameters and in the correct mode. At this
 * stage all input parameters are in this form: key value. Both key and
 * value contain no spaces and if the value does, then it is bounded by
 * apostrophes.
 *
 * @throws InvalidInputFileException
 * @throws ArgsParseException
 * @throws IOException
 */
private void parseArgsAndInitProgram() throws InvalidInputFileException, ArgsParseException, IOException {
    boolean inputAndOutputGiven = findAndReadConfigIfGivenAndSetMode();
    initGivenParameters();
    if (TaskConfig.gui) {
    /* start gui with previous set parameters */
    } else if (inputAndOutputGiven && !TaskConfig.gui) {
        ClusteringManagerTask manageTask = new ClusteringManagerTask();
        // run without initialising new thread.
        manageTask.run();
    } else {
        /* either input or output is missing */
        throw new ArgsParseException("Either input file/directory (-i) or output file (-o) is missing!");
    }
}