Java Taxa.getTaxon方法代码示例

import dr.evolution.util.Taxa; //导入方法依赖的package包/类
public static Set<String> getStatesListOfTrait(Taxa taxonList, String traitName) {
    Set<String> states = new TreeSet<String>();

    if (taxonList == null) {
        throw new IllegalArgumentException("taxon list is null");
    }

    for (int i = 0; i < taxonList.getTaxonCount(); i++) {
        Taxon taxon = taxonList.getTaxon(i);
        String attr = (String) taxon.getAttribute(traitName);

        // ? is used to denote missing data so is not a state...
        if (attr != null && !attr.equals("?")) {
            states.add(attr);
        }
    }


    return states;
}
 

import dr.evolution.util.Taxa; //导入方法依赖的package包/类
public static int getEmptyStateIndex(Taxa taxonList, String traitName) {
    if (taxonList == null) {
        throw new IllegalArgumentException("taxon list is null");
    }

    for (int i = 0; i < taxonList.getTaxonCount(); i++) {
        Taxon taxon = taxonList.getTaxon(i);
        String attr = (String) taxon.getAttribute(traitName);

        // ? is used to denote missing data so is not a state...
        if (attr == null || attr.equals("?")) {
            return i;
        }
    }

    return -1;
}
 

import dr.evolution.util.Taxa; //导入方法依赖的package包/类
public GreatCircleDistances(Taxa taxa, String attributeName) {

        distances = new double[taxa.getTaxonCount()][taxa.getTaxonCount()];

        for (int i = 0; i < taxa.getTaxonCount(); i++) {

            Taxon taxon = taxa.getTaxon(i);

            String attr = (String)taxon.getAttribute(attributeName);
            String[] loc = attr.split(" ");
            double latitude = Double.parseDouble(loc[0]);
            double longitude = Double.parseDouble(loc[1]);


            SphericalPolarCoordinates coord = new SphericalPolarCoordinates(latitude, longitude);
            //System.out.println(coord);

            for (int j = i+1; j < taxa.getTaxonCount(); j++) {
                Taxon taxon2 = taxa.getTaxon(j);
                attr = (String)taxon2.getAttribute(attributeName);
                String[] loc2 = attr.split(" ");
                latitude = Double.parseDouble(loc2[0]);
                longitude = Double.parseDouble(loc2[1]);

                SphericalPolarCoordinates coord2 = new SphericalPolarCoordinates(latitude, longitude);

                distances[i][j] = distances[j][i] = coord.distance(coord2);
            }
        }
    }
 

import dr.evolution.util.Taxa; //导入方法依赖的package包/类
private void writeTaxa(Taxa taxa, XMLWriter writer, String suffix) {

		writer.writeOpenTag(TaxaParser.TAXA, // tagname
				new Attribute[] { // attributes[]
				new Attribute.Default<String>(XMLParser.ID, TaxaParser.TAXA + suffix) });

		for (int i = 0; i < taxa.getTaxonCount(); i++) {

			Taxon taxon = taxa.getTaxon(i);

			writer.writeTag(
					TaxonParser.TAXON, // tagname
					new Attribute[] { // attributes[]
					new Attribute.Default<String>(XMLParser.ID, taxon.getId()) },
					true // close
			);

		}// END: i loop

		writer.writeCloseTag(TaxaParser.TAXA);
	}
 

import dr.evolution.util.Taxa; //导入方法依赖的package包/类
/**
 * Generate additional taxon sets
 *
 * @param writer the writer
 */
public void writeTaxonSets(XMLWriter writer) {

    writer.writeText("");
    for (Taxa taxa : taxonSets) {
        writer.writeOpenTag(
                TaxaParser.TAXA,
                new Attribute[]{
                        new Attribute.Default<String>(XMLParser.ID, taxa.getId())
                }
        );

        for (int j = 0; j < taxa.getTaxonCount(); j++) {
            Taxon taxon = taxa.getTaxon(j);

            writer.writeTag(TaxonParser.TAXON, new Attribute[]{new Attribute.Default<String>(XMLParser.IDREF, taxon.getId())}, true);
        }
        writer.writeCloseTag(TaxaParser.TAXA);
    }
}
 

import dr.evolution.util.Taxa; //导入方法依赖的package包/类
/**
 * Returns true if taxa are all found in availableTaxa
 *
 * @param taxa          a set of taxa
 * @param availableTaxa a potential superset of taxa
 * @return true if the taxa are all found in availableTaxa
 */
protected boolean isCompatible(Taxa taxa, List<Taxon> availableTaxa) {

    for (int i = 0; i < taxa.getTaxonCount(); i++) {
        Taxon taxon = taxa.getTaxon(i);
        if (!availableTaxa.contains(taxon)) {
            return false;
        }
    }
    return true;
}
 

import dr.evolution.util.Taxa; //导入方法依赖的package包/类
/**
 * Returns true if taxa are all found in availableTaxa
 * @param taxa
 * @param availableTaxa
 * @return true if the taxa are all found in availableTaxa
 */
private boolean isCompatible(Taxa taxa, List availableTaxa) {

    for (int i = 0; i < taxa.getTaxonCount(); i++) {
        Taxon taxon = taxa.getTaxon(i);
        if (!availableTaxa.contains(taxon)) {
            return false;
        }
    }
    return true;
}
 

import dr.evolution.util.Taxa; //导入方法依赖的package包/类
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;
    }
 

import dr.evolution.util.Taxa; //导入方法依赖的package包/类
public static void printTaxaSet(Taxa taxa) {
	for (int i = 0; i < taxa.getTaxonCount(); i++) {
		Taxon taxon = taxa.getTaxon(i);
		System.out.print("\t\t " + taxonToString(taxon, false) + ("\n"));
	}
}
 

import dr.evolution.util.Taxa; //导入方法依赖的package包/类
public static String taxaToString(Taxa taxa, boolean printNames) {

		String string = "";

		for (int i = 0; i < taxa.getTaxonCount(); i++) {

			Taxon taxon = taxa.getTaxon(i);
			string += taxonToString(taxon, printNames) + ("\n");

		}

		return string;
	}