Examples with SiteModel dr.oldevomodel.sitemodel.SiteModel used on opensource projects

Example 11 with SiteModel

use of dr.oldevomodel.sitemodel.SiteModel in project beast-mcmc by beast-dev.

the class SequenceSimulator method main.

// getDefaultSiteModel
public static void main(String[] args) {
    try {
        int nReplications = 10;
        // create tree
        NewickImporter importer = new NewickImporter("((A:1.0,B:1.0)AB:1.0,(C:1.0,D:1.0)CD:1.0)ABCD;");
        Tree tree = importer.importTree(null);
        // create site model
        SiteModel siteModel = getDefaultSiteModel();
        // create branch rate model
        BranchRateModel branchRateModel = new DefaultBranchRateModel();
        // feed to sequence simulator and generate leaves
        SequenceSimulator treeSimulator = new SequenceSimulator(tree, siteModel, branchRateModel, nReplications);
        Sequence ancestralSequence = new Sequence();
        ancestralSequence.appendSequenceString("TCAGGTCAAG");
        treeSimulator.setAncestralSequence(ancestralSequence);
        System.out.println(treeSimulator.simulate().toString());
    } catch (Exception e) {
        e.printStackTrace();
    }
//END: try-catch block
}