Example usage for org.apache.commons.cli2 CommandLine getValue

Introduction

In this page you can find the example usage for org.apache.commons.cli2 CommandLine getValue.

Prototype

Object getValue(final Option option) throws IllegalStateException;

Source Link

Document

Retrieves the single Argument value associated with the specified Option

Usage

From source file:com.martinkampjensen.thesis.Main.java

private static void check(CommandLine cmdLine) {
    final String fileName = (String) cmdLine.getValue(_oCheck);
    final File file = new File(fileName);

    Application.check(file);//from  w  w  w .j  ava  2 s  .c  o  m
}

From source file:com.martinkampjensen.thesis.Main.java

private static void execute(CommandLine cmdLine) {
    final String fileName = (String) cmdLine.getValue(_oExecute);
    final File file = new File(fileName);

    Application.execute(file);// w w  w .ja v  a  2s .c o m
}

From source file:com.martinkampjensen.thesis.Main.java

private static void evaluate(CommandLine cmdLine) {
    final String fileOrClassName = (String) cmdLine.getValue(_oEvaluate);
    final Model model = Util.instantiateModel(fileOrClassName);

    Application.evaluate(model);//from  w  ww.j a va  2s . co  m
}

From source file:com.martinkampjensen.thesis.Main.java

private static void print(CommandLine cmdLine) {
    final String fileOrClassName = (String) cmdLine.getValue(_oPrint);
    final Model model = Util.instantiateModel(fileOrClassName);

    Application.print(model);/*from ww  w.  j a v a 2 s. c o  m*/
}

From source file:com.martinkampjensen.thesis.Main.java

private static void visualize(CommandLine cmdLine) {
    final String fileOrClassName = (String) cmdLine.getValue(_oVisualize);
    final Model model = Util.instantiateModel(fileOrClassName);

    Application.visualize(model);//w w  w . j a  v  a  2 s .c o  m
}

From source file:com.martinkampjensen.thesis.Main.java

private static void minimize(CommandLine cmdLine) {
    final String fileOrClassName = (String) cmdLine.getValue(_oMinimize);
    final Model model = Util.instantiateModel(fileOrClassName);
    final boolean random = cmdLine.hasOption(_oMinimizeRandom);

    Application.minimize(model, random);
}

From source file:com.martinkampjensen.thesis.Main.java

private static void analyze(CommandLine cmdLine) {
    final String fileOrClassName = (String) cmdLine.getValue(_oAnalyze);
    final Model model = Util.instantiateModel(fileOrClassName);
    final String output = (String) cmdLine.getValue(_oAnalyzeOutput);
    final File file = (output == null ? null : new File(output));

    Application.analyze(model, file);//from   w  w w  .  j av  a  2 s.  co  m
}

From source file:com.martinkampjensen.thesis.Main.java

private static void sample(CommandLine cmdLine) {
    final String fileOrClassName = (String) cmdLine.getValue(_oSample);
    final Model model = Util.instantiateModel(fileOrClassName);
    final int[] angleIds = parseIntArray(cmdLine, _oSampleAngleIds);
    final boolean random = cmdLine.hasOption(_oSampleRandom);

    Application.sample(model, angleIds, random);
}

From source file:com.martinkampjensen.thesis.Main.java

private static void extract(CommandLine cmdLine) {
    final String fileName = (String) cmdLine.getValue(_oExtract);
    final int[] conformationIds = parseIntArray(cmdLine, _oExtractConformation);
    final String trajectory = (String) cmdLine.getValue(_oExtractTrajectory);

    final File trajectoryFile = (trajectory == null ? null : new File(trajectory));

    if (trajectoryFile != null) {
        if (conformationIds.length != 2) {
            errorExit("Specify exactly two ids", StatusCode.ARGUMENT);
        }/* w  w w  . ja v  a2  s .co m*/

        Application.extract(new File(fileName), conformationIds[0], conformationIds[1], trajectoryFile);
    } else {
        Application.extract(new File(fileName), conformationIds);
    }
}

From source file:com.martinkampjensen.thesis.Main.java

private static void barriers(CommandLine cmdLine) {
    final String fileOrClassName = (String) cmdLine.getValue(_oBarriers);
    final String postScript = (String) cmdLine.getValue(_oBarriersPostScript);
    final String structure = (String) cmdLine.getValue(_oBarriersStructure);
    final File moleculeFile = new File(fileOrClassName);
    final File postScriptFile = (postScript == null ? null : new File(postScript));
    final File structureFile = (structure == null ? null : new File(structure));

    if (cmdLine.hasOption(_oBarriersTrajectory)) {
        final String trajectory = (String) cmdLine.getValue(_oBarriersTrajectory);
        final String energy = (String) cmdLine.getValue(_oBarriersEnergy);
        final File trajectoryFile = new File(trajectory);
        final File energyFile = new File(energy);
        final double pruning = parseDouble(cmdLine, _oBarriersPruning);
        final double neighbor = parseDouble(cmdLine, _oBarriersNeighbor);
        Application.barriers(moleculeFile, trajectoryFile, energyFile, postScriptFile, structureFile, pruning,
                neighbor);//from  w w w.  j a  v a2  s  .co m
    } else {
        final String topology = (String) cmdLine.getValue(_oBarriersTopology);
        final File topologyFile = (topology == null ? null : new File(topology));
        final Model model = Util.instantiateModel(fileOrClassName, topologyFile);
        Application.barriers(moleculeFile, model, postScriptFile, structureFile);
    }
}