Examples with Taxa dr.evolution.util.Taxa used on opensource projects

Example 56 with Taxa

use of dr.evolution.util.Taxa in project beast-mcmc by beast-dev.

the class VariableCoalescentSimulator method readSampleFile.

private static Taxa readSampleFile(String fileName, double generationTime) throws IOException {
    BufferedReader reader = new BufferedReader(new FileReader(fileName));
    String line = reader.readLine();
    Taxa taxa = new Taxa();
    int id = 0;
    while (line != null) {
        if (!line.startsWith("#")) {
            String[] tokens = line.split("[\t ]+");
            // sample times are in the same units as simulation
            double sampleTime = Double.parseDouble(tokens[0]) / generationTime;
            int count = Integer.parseInt(tokens[1]);
            for (int i = 0; i < count; i++) {
                Taxon taxon = new Taxon(id + "");
                taxon.setAttribute(dr.evolution.util.Date.DATE, new Date(sampleTime, Units.Type.GENERATIONS, true));
                taxa.addTaxon(taxon);
                id += 1;
            }
        }
        line = reader.readLine();
    }
    return taxa;
}

Example 57 with Taxa

use of dr.evolution.util.Taxa in project beast-mcmc by beast-dev.

the class GibbsIndependentCoalescentOperator method doOperation.

/**
	 * change the parameter and return the hastings ratio.
     */
public double doOperation() {
    CoalescentSimulator simulator = new CoalescentSimulator();
    List<TaxonList> taxonLists = new ArrayList<TaxonList>();
    double rootHeight = -1.0;
    double oldLikelihood = 0.0;
    double newLikelihood = 0.0;
    // should have one child that is node
    for (int i = 0; i < xo.getChildCount(); i++) {
        final Object child = xo.getChild(i);
        //careful: Trees are TaxonLists ... (AER); see OldCoalescentSimulatorParser
        if (child instanceof Tree) {
        //do nothing
        } else if (child instanceof TaxonList) {
            //taxonLists.add((TaxonList) child);
            taxonLists.add((Taxa) child);
            //taxa added
            break;
        }
    }
    try {
        Tree[] trees = new Tree[taxonLists.size()];
        // simulate each taxonList separately
        for (int i = 0; i < taxonLists.size(); i++) {
            trees[i] = simulator.simulateTree(taxonLists.get(i), demoModel);
        }
        oldLikelihood = coalescent.getLogLikelihood();
        SimpleTree simTree = simulator.simulateTree(trees, demoModel, rootHeight, trees.length != 1);
        //this would be the normal way to do it
        treeModel.beginTreeEdit();
        //now it's allowed to adjust the tree structure
        treeModel.adoptTreeStructure(simTree);
        //endTreeEdit() would then fire the events
        treeModel.endTreeEdit();
        newLikelihood = coalescent.getLogLikelihood();
    } catch (IllegalArgumentException iae) {
        try {
            throw new XMLParseException(iae.getMessage());
        } catch (XMLParseException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }
    }
    //return oldLikelihood - newLikelihood;
    return 0;
}

Example 58 with Taxa

use of dr.evolution.util.Taxa in project beast-mcmc by beast-dev.

the class ExternalLengthStatisticParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    String name = xo.getAttribute(Statistic.NAME, xo.getId());
    Tree tree = (Tree) xo.getChild(Tree.class);
    TaxonList taxa = (TaxonList) xo.getChild(Taxa.class);
    try {
        return new ExternalLengthStatistic(name, tree, taxa);
    } catch (TreeUtils.MissingTaxonException mte) {
        throw new XMLParseException("Taxon, " + mte + ", in " + getParserName() + "was not found in the tree.");
    }
}

Example 59 with Taxa

use of dr.evolution.util.Taxa in project beast-mcmc by beast-dev.

the class RandomSubsetTaxaParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Taxa originalTaxa = new Taxa();
    for (int i = 0; i < xo.getChildCount(); i++) {
        Object child = xo.getChild(i);
        if (child instanceof Taxon) {
            Taxon taxon = (Taxon) child;
            originalTaxa.addTaxon(taxon);
        } else if (child instanceof TaxonList) {
            TaxonList taxonList1 = (TaxonList) child;
            for (int j = 0; j < taxonList1.getTaxonCount(); j++) {
                originalTaxa.addTaxon(taxonList1.getTaxon(j));
            }
        } else {
            throwUnrecognizedElement(xo);
        }
    }
    List<Taxon> originalTaxonList = originalTaxa.asList();
    int sampleTotal = xo.getAttribute(COUNT, originalTaxonList.size());
    if (sampleTotal < 2) {
        throw new XMLParseException("Must sample atleast two taxa");
    }
    boolean withReplacement = xo.getAttribute(WITH_REPLACEMENT, false);
    Taxa sampledTaxa = new Taxa();
    for (int i = 0; i < sampleTotal; i++) {
        int choice = MathUtils.nextInt(originalTaxonList.size());
        Taxon taxonToAdd = originalTaxonList.get(choice);
        sampledTaxa.addTaxon(taxonToAdd);
        if (!withReplacement) {
            originalTaxonList.remove(choice);
        }
    }
    return sampledTaxa;
}

Example 60 with Taxa

use of dr.evolution.util.Taxa in project beast-mcmc by beast-dev.

the class RandomTaxaSampleParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Taxa population = (Taxa) xo.getChild(Taxa.class);
    int n = xo.getIntegerAttribute(SAMPLE);
    int N = population.getTaxonCount();
    if (n <= 0 || n > N) {
        throw new XMLParseException("sample must be greater than 0 and less than or equal to the population size");
    }
    Taxa sample = new Taxa();
    ArrayList<Integer> indexes = new ArrayList<Integer>(N);
    for (int i = 0; i < N; i++) indexes.add(i);
    Logger.getLogger("dr.evolution").info("Generating a random taxa sample of size: " + n);
    for (int i = 0; i < n; i++) {
        int randomIndex = MathUtils.nextInt(indexes.size());
        Taxon selectedTaxon = population.getTaxon(indexes.get(randomIndex));
        sample.addTaxon(selectedTaxon);
        indexes.remove(randomIndex);
    }
    if (xo.hasAttribute(PRINT_TAXA) && xo.getBooleanAttribute(PRINT_TAXA)) {
        String fileName = null;
        if (xo.hasAttribute(FILE_NAME)) {
            fileName = xo.getStringAttribute(FILE_NAME);
        }
        if (fileName != null) {
            try {
                Writer write;
                File file = new File(fileName);
                String name = file.getName();
                String parent = file.getParent();
                if (!file.isAbsolute()) {
                    parent = System.getProperty("user.dir");
                }
                write = new FileWriter(new File(parent, name));
                write.write("<taxa id=\"randomTaxaSample\">\n");
                for (int i = 0; i < n; i++) {
                    write.write("\t<taxon idref=\"" + sample.getTaxonId(i) + "\"/>\n");
                }
                write.write("</taxa id=\"randomTaxaSample\">\n");
                write.flush();
            } catch (IOException fnfe) {
                throw new XMLParseException("File '" + fileName + "' can not be opened for " + getParserName() + " element.");
            }
        } else {
            Logger.getLogger("dr.evomodel").info("<taxa id=\"randomTaxaSample\">");
            for (int i = 0; i < n; i++) {
                Logger.getLogger("dr.evomodel").info("\t<taxon idref=\" " + sample.getTaxonId(i) + " \"> ");
            }
            Logger.getLogger("dr.evomodel").info("</taxa id=\"randomTaxaSample\">");
        }
    }
    return sample;
}