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

Example 16 with PartitionSubstitutionModel

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

the class NexusApplicationImporter method parseMrBayesBlock.

/**
     * Parses a 'MRBAYES' block.
     *
     * @param options  the BEAUti options
     * @param charSets a list of char sets to *add* to if any are defined in PAUP block
     * @return a partition model representing the model defined in the MRBAYES block
     * @throws dr.evolution.io.Importer.ImportException
     *                             if MRBAYES block is poorly formed
     * @throws java.io.IOException if I/O fails
     */
public PartitionSubstitutionModel parseMrBayesBlock(BeautiOptions options, List<CharSet> charSets) throws ImportException, IOException {
    PartitionSubstitutionModel model = new PartitionSubstitutionModel(options, "nucs");
    readTopLevelBlock(options, model, charSets);
    return model;
}

Example 17 with PartitionSubstitutionModel

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

the class NexusApplicationImporter method parsePAUPBlock.

/**
     * Parses a 'PAUP' block.
     *
     * @param options  the BEAUti options
     * @param charSets a list of char sets to *add* to if any are defined in PAUP block
     * @return a partition model representing the model defined in the PAUP block
     * @throws dr.evolution.io.Importer.ImportException
     *                             if PAUP block is poorly formed
     * @throws java.io.IOException if I/O fails
     */
public PartitionSubstitutionModel parsePAUPBlock(BeautiOptions options, List<CharSet> charSets) throws ImportException, IOException {
    PartitionSubstitutionModel model = new PartitionSubstitutionModel(options, "nucs");
    readTopLevelBlock(options, model, charSets);
    return model;
}