be.svlandeg.diffany.console.DiffanyOptions.java Source code

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Here is the source code for be.svlandeg.diffany.console.DiffanyOptions.java

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package be.svlandeg.diffany.console;

/*
 * #%L
 * Diffany
 * %%
 * Copyright (C) 2014 PSB/UGent - Sofie Van Landeghem and Thomas Van Parys
 * %%
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU Lesser General Public License as
 * published by the Free Software Foundation, either version 3 of the
 * License, or (at your option) any later version.
 * 
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Lesser Public License for more details.
 * 
 * You should have received a copy of the GNU General Lesser Public
 * License along with this program.  If not, see
 * <http://www.gnu.org/licenses/lgpl-3.0.html>.
 * #L%
 */

import java.util.HashSet;
import java.util.Set;

import org.apache.commons.cli.Option;
import org.apache.commons.cli.OptionBuilder;
import org.apache.commons.cli.Options;

/**
 * This class defines the various options available when running the Diffany algorithms through the console.
 * 
 * @author Sofie Van Landeghem
 */
public class DiffanyOptions {

    private Options options;

    protected static String logShort = "l";

    protected static String cutoffShort = "c";
    protected static String operatorShort = "oper";
    protected static String modeShort = "m";

    protected static String headerShort = "h";

    protected static String inputShort = "i";
    protected static String outputShort = "o";

    protected static String runDiff = "diff";
    protected static String runCons = "cons";
    protected static String nextID = "ID";

    protected static boolean defaultRunDiff = true;
    protected static boolean defaultRunCons = true;

    protected static boolean defaultMinOperator = true;
    protected static boolean defaultModePairwise = false;

    protected static boolean defaultReadHeader = true;

    /**
     * Constructor initializes the options available in Diffany
     */
    public DiffanyOptions() {
        defineOptions();
    }

    /**
     * Retrieve the options object for the Diffany project
     * @return the Diffany options object
     */
    public Options getDiffanyOptions() {
        return options;
    }

    /**
     * Define the options available in the Diffany project
     */
    private void defineOptions() {
        options = new Options();
        for (Option o : getAllFlags()) {
            options.addOption(o);
        }
        for (Option o : getAllParameters()) {
            options.addOption(o);
        }
    }

    /**
     * Define the flag options available in the Diffany project
     */
    private Set<Option> getAllFlags() {
        boolean hasArgument = false;
        Set<Option> allFlags = new HashSet<Option>();

        allFlags.add(new Option(logShort, "log", hasArgument, "display a progress/log file during the run"));

        return allFlags;
    }

    /**
     * Define the options specifying necessary arguments for the Diffany algorithms
     */
    private Set<Option> getAllParameters() {
        Set<Option> allParameters = new HashSet<Option>();

        OptionBuilder.withArgName("dir");
        OptionBuilder.withLongOpt("inputDir");
        OptionBuilder.hasArgs(1);
        OptionBuilder.isRequired();
        OptionBuilder
                .withDescription("the input directory containing the reference and condition-specific networks");
        allParameters.add(OptionBuilder.create(inputShort));

        OptionBuilder.withArgName("dir");
        OptionBuilder.withLongOpt("outputDir");
        OptionBuilder.hasArgs(1);
        OptionBuilder.isRequired();
        OptionBuilder.withDescription(
                "the output directory which will contain the generated differential/consensus networks");
        allParameters.add(OptionBuilder.create(outputShort));

        String defaultRunDiffString = defaultRunDiff ? "yes" : "no";
        OptionBuilder.withLongOpt("differential");
        OptionBuilder.hasArgs(1);
        OptionBuilder.withDescription("whether or not to calculate differential networks: yes or no (default="
                + defaultRunDiffString + ")");
        allParameters.add(OptionBuilder.create(runDiff));

        String defaultRunConsString = defaultRunCons ? "yes" : "no";
        ;
        OptionBuilder.withLongOpt("consensus");
        OptionBuilder.hasArgs(1);
        OptionBuilder.withDescription(
                "whether or not to calculate consensus networks: yes or no (default=" + defaultRunConsString + ")");
        allParameters.add(OptionBuilder.create(runCons));

        OptionBuilder.withLongOpt("outputID");
        OptionBuilder.hasArgs(1);
        OptionBuilder.withDescription("the first ID that will be used for the generated networks");
        allParameters.add(OptionBuilder.create(nextID));

        OptionBuilder.withLongOpt("confidence");
        OptionBuilder.hasArgs(1);
        OptionBuilder.withDescription(
                "the minimum confidence threshold for output edges, as an integer or double (default=0.0)");
        allParameters.add(OptionBuilder.create(cutoffShort));

        String defaultMinOperatorString = defaultMinOperator ? "min" : "max";
        OptionBuilder.withLongOpt("operator");
        OptionBuilder.hasArgs(1);
        OptionBuilder.withDescription("the operator used to create consensus edges: min or max (default="
                + defaultMinOperatorString + ")");
        allParameters.add(OptionBuilder.create(operatorShort));

        String defaultModeString = defaultModePairwise ? "pairwise" : "all";
        OptionBuilder.withLongOpt("mode");
        OptionBuilder.hasArgs(1);
        OptionBuilder
                .withDescription("the mode of comparison: pairwise or all (default=" + defaultModeString + ")");
        allParameters.add(OptionBuilder.create(modeShort));

        String defaultHeaderString = defaultReadHeader ? "yes" : "no";
        OptionBuilder.withLongOpt("skipHeader");
        OptionBuilder.hasArgs(1);
        OptionBuilder.withDescription(
                "whether or not to skip the first line (header) in the network .txt files (default="
                        + defaultHeaderString + ")");
        allParameters.add(OptionBuilder.create(headerShort));

        return allParameters;
    }
}