Examples with BeautiOptions dr.app.beauti.options.BeautiOptions used on opensource projects

Example 1 with BeautiOptions

use of dr.app.beauti.options.BeautiOptions in project beast-mcmc by beast-dev.

the class BeautiTesterConfig method createOptions.

public BeautiOptions createOptions() {
    BeautiOptions beautiOptions = new BeautiOptions();
    beautiOptions.fileNameStem = "";
    beautiOptions.treeFileName.clear();
    beautiOptions.substTreeLog = false;
    beautiOptions.substTreeFileName.clear();
    // MCMC options
    beautiOptions.chainLength = 100;
    beautiOptions.logEvery = 100;
    beautiOptions.echoEvery = 100;
    beautiOptions.burnIn = 10;
    beautiOptions.fileName = null;
    beautiOptions.autoOptimize = true;
    // Data options
    beautiOptions.taxonList = null;
    beautiOptions.datesUnits = DateUnitsType.YEARS;
    beautiOptions.datesDirection = DateUnitsType.FORWARDS;
    //        beautiOptions.startingTreeType = StartingTreeType.RANDOM;
    //        beautiOptions.fixedTree = false;
    beautiOptions.performTraceAnalysis = false;
    // until beuati button
    beautiOptions.generateCSV = true;
    beautiOptions.units = Units.Type.SUBSTITUTIONS;
    beautiOptions.maximumTipHeight = 0.0;
    //        beautiOptions.meanSubstitutionRate = 1.0;
    //        beautiOptions.fixedSubstitutionRate = true;
    generator = new BeastGenerator(beautiOptions, null);
    return beautiOptions;
}