Examples with Nucleotides dr.evolution.datatype.Nucleotides used on opensource projects

Example 1 with Nucleotides

use of dr.evolution.datatype.Nucleotides in project beast-mcmc by beast-dev.

the class BeagleSequenceSimulatorParser method parseXMLObject.

// END: getSyntaxRules
@Override
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    String msg = "";
    boolean parallel = false;
    boolean outputAncestralSequences = false;
    if (xo.hasAttribute(PARALLEL)) {
        parallel = xo.getBooleanAttribute(PARALLEL);
    }
    if (xo.hasAttribute(OUTPUT_ANCESTRAL_SEQUENCES)) {
        outputAncestralSequences = xo.getBooleanAttribute(OUTPUT_ANCESTRAL_SEQUENCES);
    }
    SimpleAlignment.OutputType output = SimpleAlignment.OutputType.FASTA;
    if (xo.hasAttribute(OUTPUT)) {
        output = SimpleAlignment.OutputType.parseFromString(xo.getStringAttribute(OUTPUT));
    }
    int siteCount = 0;
    int to = 0;
    for (int i = 0; i < xo.getChildCount(); i++) {
        Partition partition = (Partition) xo.getChild(i);
        to = partition.to + 1;
        if (to > siteCount) {
            siteCount = to;
        }
    }
    // END: partitions loop
    ArrayList<Partition> partitionsList = new ArrayList<Partition>();
    for (int i = 0; i < xo.getChildCount(); i++) {
        Partition partition = (Partition) xo.getChild(i);
        if (partition.from > siteCount) {
            throw new XMLParseException("Illegal 'from' attribute in " + PartitionParser.PARTITION + " element");
        }
        if (partition.to > siteCount) {
            throw new XMLParseException("Illegal 'to' attribute in " + PartitionParser.PARTITION + " element");
        }
        if (partition.to == -1) {
            partition.to = siteCount - 1;
        }
        if (partition.getRootSequence() != null) {
            // TODO: what about 'every'?
            int partitionSiteCount = (partition.to - partition.from) + 1;
            if (partition.getRootSequence().getLength() != 3 * partitionSiteCount && partition.getFreqModel().getDataType() instanceof Codons) {
                throw new RuntimeException("Root codon sequence " + "for partition " + (i + 1) + " has " + partition.getRootSequence().getLength() + " characters " + "expecting " + 3 * partitionSiteCount + " characters");
            } else if (partition.getRootSequence().getLength() != partitionSiteCount && partition.getFreqModel().getDataType() instanceof Nucleotides) {
                throw new RuntimeException("Root nuleotide sequence " + "for partition " + (i + 1) + " has " + partition.getRootSequence().getLength() + " characters " + "expecting " + partitionSiteCount + " characters");
            }
        // END: dataType check
        // System.exit(-1);
        }
        // END: ancestralSequence check
        partitionsList.add(partition);
    }
    // END: partitions loop
    msg += "\n\t" + partitionsList.size() + " partitions with a total of ";
    msg += siteCount + ((siteCount > 1) ? " replications " : " replication");
    if (msg.length() > 0) {
        Logger.getLogger("dr.app.beagle.tools").info("\nUsing Beagle Sequence Simulator: " + msg + "\n");
    }
    BeagleSequenceSimulator s = new BeagleSequenceSimulator(partitionsList);
    SimpleAlignment alignment = s.simulate(parallel, outputAncestralSequences);
    alignment.setOutputType(output);
    return alignment;
}