Java XMLParser类代码示例

import dr.xml.XMLParser; //导入依赖的package包/类
private void writeGeneralDataType(PartitionSubstitutionModel model, XMLWriter writer) {

        writer.writeComment("general data type for discrete trait model, '" + model.getName() + "'");

        Set<String> states = options.getStatesForDiscreteModel(model);
        String prefix = model.getName() + ".";

        // <generalDataType>
        writer.writeOpenTag(GeneralDataTypeParser.GENERAL_DATA_TYPE, new Attribute[]{
                new Attribute.Default<String>(XMLParser.ID, prefix + "dataType")});

        int numOfStates = states.size();
        writer.writeComment("Number Of States = " + numOfStates);

        for (String eachGD : states) {
            writer.writeTag(GeneralDataTypeParser.STATE, new Attribute[]{
                    new Attribute.Default<String>(GeneralDataTypeParser.CODE, eachGD)}, true);
        }

        writer.writeCloseTag(GeneralDataTypeParser.GENERAL_DATA_TYPE);
    }
 

import dr.xml.XMLParser; //导入依赖的package包/类
/**
 * Generate a taxa block from these beast options
 *
 * @param writer    the writer
 * @param taxonList the taxon list to write
 * @throws dr.app.util.Arguments.ArgumentException
 *          ArgumentException
 */
private void writeTaxa(TaxonList taxonList, XMLWriter writer) throws Arguments.ArgumentException {
    // -1 (single taxa), 0 (1st gene of multi-taxa)

    writer.writeComment("The list of taxa to be analysed (can also include dates/ages).",
            "ntax=" + taxonList.getTaxonCount());
    writer.writeOpenTag(TaxaParser.TAXA, new Attribute[]{new Attribute.Default<String>(XMLParser.ID, TaxaParser.TAXA)});

    boolean hasAttr = options.traits.size() > 0;

    boolean firstDate = true;
    for (int i = 0; i < taxonList.getTaxonCount(); i++) {
        Taxon taxon = taxonList.getTaxon(i);

        boolean hasDate = false;
        if (options.clockModelOptions.isTipCalibrated()) {
            hasDate = TaxonList.Utils.hasAttribute(taxonList, i, dr.evolution.util.Date.DATE);
        }

        if (hasDate) {
            dr.evolution.util.Date date = (dr.evolution.util.Date) taxon.getAttribute(dr.evolution.util.Date.DATE);

            if (firstDate) {
                options.units = date.getUnits();
                firstDate = false;
            } else {
                if (options.units != date.getUnits()) {
                    System.err.println("Error: Units in dates do not match.");
                }
            }
        }

        writeTaxon(taxon, hasDate, hasAttr, writer);

    }

    writer.writeCloseTag(TaxaParser.TAXA);
}
 

import dr.xml.XMLParser; //导入依赖的package包/类
public void writeDifferentTaxa(AbstractPartitionData dataPartition, XMLWriter writer) {
    TaxonList taxonList = dataPartition.getTaxonList();

    String name = dataPartition.getPartitionTreeModel().getName();

    writer.writeComment("gene name = " + name + ", ntax= " + taxonList.getTaxonCount());
    writer.writeOpenTag(TaxaParser.TAXA, new Attribute[]{new Attribute.Default<String>(XMLParser.ID, name + "." + TaxaParser.TAXA)});

    for (int i = 0; i < taxonList.getTaxonCount(); i++) {
        if ( !(dataPartition instanceof PartitionPattern && ((PartitionPattern) dataPartition).getPatterns().isMasked(i) ) ) {
            final Taxon taxon = taxonList.getTaxon(i);
            writer.writeIDref(TaxonParser.TAXON, taxon.getId());
        }
    }

    writer.writeCloseTag(TaxaParser.TAXA);
}
 

import dr.xml.XMLParser; //导入依赖的package包/类
/**
 * write tag <sp>
 *
 * @param taxonList TaxonList
 * @param writer    XMLWriter
 */
private void writeMultiSpecies(TaxonList taxonList, XMLWriter writer) {
    List<String> species = options.starBEASTOptions.getSpeciesList();
    String sp;

    numOfSpecies = species.size(); // used in private String getIndicatorsParaValue()

    for (String eachSp : species) {
        writer.writeOpenTag(SpeciesBindingsSPinfoParser.SP, new Attribute[]{new Attribute.Default<String>(XMLParser.ID, eachSp)});

        for (int i = 0; i < taxonList.getTaxonCount(); i++) {
            Taxon taxon = null;
            try {
                taxon = taxonList.getTaxon(i);
                sp = taxon.getAttribute(TraitData.TRAIT_SPECIES).toString();
            } catch (Exception e) {
                throw new IllegalArgumentException("Cannot get value from Taxon " + taxon.getId());
            }

            if (sp.equals(eachSp)) {
                writer.writeIDref(TaxonParser.TAXON, taxon.getId());
            }
        }
        writer.writeCloseTag(SpeciesBindingsSPinfoParser.SP);
    }

    writeGeneTrees(writer);
}
 

import dr.xml.XMLParser; //导入依赖的package包/类
/**
 * write a parameter
 *
 * @param parameterId     the parameter name/id
 * @param parameterColumn the parameter column from which the samples are taken
 * @param fileName        the file from which the samples are taken
 * @param burnin          the number of samples to be discarded
 * @param writer          the writer
 */
public void writeParameter(String parameterId, String parameterColumn, String fileName, int burnin, XMLWriter writer) {
    ArrayList<Attribute.Default> attributes = new ArrayList<Attribute.Default>();
    attributes.add(new Attribute.Default<String>(XMLParser.ID, parameterId));

    attributes.add(new Attribute.Default<String>("parameterColumn", parameterColumn));
    attributes.add(new Attribute.Default<String>("fileName", fileName));
    attributes.add(new Attribute.Default<String>("burnin", "" + burnin));

    Attribute[] attrArray = new Attribute[attributes.size()];
    for (int i = 0; i < attrArray.length; i++) {
        attrArray[i] = attributes.get(i);
    }

    writer.writeTag(ParameterParser.PARAMETER, attrArray, true);
}
 

import dr.xml.XMLParser; //导入依赖的package包/类
private void writeTaxaRef(String taxaId, PartitionTreeModel model, XMLWriter writer) {

        Attribute[] taxaAttribute = {new Attribute.Default<String>(XMLParser.IDREF, taxaId)};

        if (options.taxonSets != null && options.taxonSets.size() > 0 && !options.useStarBEAST) { // need !options.useStarBEAST,
            // *BEAST case is in STARBEASTGenerator.writeStartingTreeForCalibration(XMLWriter writer)
            writer.writeOpenTag(OldCoalescentSimulatorParser.CONSTRAINED_TAXA);
            writer.writeTag(TaxaParser.TAXA, taxaAttribute, true);
            for (Taxa taxa : options.taxonSets) {
                if (options.taxonSetsTreeModel.get(taxa).equals(model)) {
                    Parameter statistic = options.getStatistic(taxa);

                    Attribute mono = new Attribute.Default<Boolean>(
                            OldCoalescentSimulatorParser.IS_MONOPHYLETIC, options.taxonSetsMono.get(taxa));

                    writer.writeOpenTag(OldCoalescentSimulatorParser.TMRCA_CONSTRAINT, mono);

                    writer.writeIDref(TaxaParser.TAXA, taxa.getId());

                    if (model.getPartitionTreePrior().getNodeHeightPrior() == TreePriorType.YULE_CALIBRATION
                            && statistic.priorType == PriorType.UNIFORM_PRIOR) {
                        writeDistribution(statistic, false, writer);
                    }

                    writer.writeCloseTag(OldCoalescentSimulatorParser.TMRCA_CONSTRAINT);
                }
            }
            writer.writeCloseTag(OldCoalescentSimulatorParser.CONSTRAINED_TAXA);
        } else {
            writer.writeTag(TaxaParser.TAXA, taxaAttribute, true);
        }
    }
 

import dr.xml.XMLParser; //导入依赖的package包/类
private Attribute[] getModelAttributes(HierarchicalPhylogeneticModel hpm) {
    switch (hpm.getPriorType()){
        case NORMAL_HPM_PRIOR:
            return new Attribute[] {
                    new Attribute.Default<String>(XMLParser.ID, getModelName(hpm)),
            };
        case LOGNORMAL_HPM_PRIOR:
            return new Attribute[] {
                    new Attribute.Default<String>(XMLParser.ID, getModelName(hpm)),
                    //new Attribute.Default<Boolean>(LogNormalDistributionModelParser.MEAN_IN_REAL_SPACE, false),
            };
        default:
    }
    throw new RuntimeException("Unimplemented HPM prior type");
}
 

import dr.xml.XMLParser; //导入依赖的package包/类
private Attribute[] getMeanPriorAttributes(HierarchicalPhylogeneticModel hpm) {
    return new Attribute[] {
            new Attribute.Default<String>(XMLParser.ID, getMeanPriorName(hpm)),
            new Attribute.Default<Double>(PriorParsers.MEAN, hpm.getConditionalParameterList().get(0).mean),
            new Attribute.Default<Double>(PriorParsers.STDEV, hpm.getConditionalParameterList().get(0).stdev),
    };
}
 

import dr.xml.XMLParser; //导入依赖的package包/类
private Attribute[] getPrecisionPriorAttributes(HierarchicalPhylogeneticModel hpm) {
    return new Attribute[] {
            new Attribute.Default<String>(XMLParser.ID, getPrecisionPriorName(hpm)),
            new Attribute.Default<Double>(PriorParsers.SHAPE, hpm.getConditionalParameterList().get(1).shape),
            new Attribute.Default<Double>(PriorParsers.SCALE, hpm.getConditionalParameterList().get(1).scale),
            new Attribute.Default<Double>(PriorParsers.OFFSET, 0.0),
    };
}
 

import dr.xml.XMLParser; //导入依赖的package包/类
private Sequence readSequence(Element e, TaxonList taxa) throws Importer.ImportException {

        String taxonID = e.getChild(TaxonParser.TAXON).getAttributeValue(XMLParser.IDREF);
        int index = taxa.getTaxonIndex(taxonID);
        if (index < 0) {
            throw new Importer.ImportException("Unknown taxon, " + taxonID + ", in alignment");
        }
        Taxon taxon = taxa.getTaxon(index);

        String[] seq = e.getTextTrim().split("\\s");
        StringBuilder sb = new StringBuilder();
        for (String part : seq) {
            sb.append(part);
        }

        return new Sequence(taxon, sb.toString());
    }
 

import dr.xml.XMLParser; //导入依赖的package包/类
private void writeNewick(TreeModel tree, XMLWriter writer,
		String suffix) {

	writer.writeOpenTag(NewickParser.NEWICK,
			new Attribute[] { new Attribute.Default<String>(XMLParser.ID,
					Utils.TOPOLOGY + suffix), //
					new Attribute.Default<String>(NewickParser.USING_DATES,
							"false"), //
							new Attribute.Default<String>(NewickParser.USING_HEIGHTS,
									"true") //
	});

	writer.writeText(TreeUtils.newick(tree));

	writer.writeCloseTag(NewickParser.NEWICK);

}
 

import dr.xml.XMLParser; //导入依赖的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.xml.XMLParser; //导入依赖的package包/类
private void writeTreeModel(
//			TreeModel tree, 
			XMLWriter writer, String suffix) {

		final String treeModelName = TreeModel.TREE_MODEL + suffix;

		writer.writeTag(TreeModel.TREE_MODEL, new Attribute.Default<String>(
				XMLParser.ID, treeModelName), false);

		writer.writeIDref("tree", Utils.TOPOLOGY + suffix);

		writeParameter(TreeModelParser.ROOT_HEIGHT, treeModelName + "."
				+ TreeModelParser.ROOT_HEIGHT, 1, null, writer);

		writer.writeOpenTag(TreeModelParser.NODE_HEIGHTS,
				new Attribute.Default<String>(TreeModelParser.INTERNAL_NODES,
						"true"));

		writeParameter(null, treeModelName + "." + "internalNodeHeights", 1,
				null, writer);

		writer.writeCloseTag(TreeModelParser.NODE_HEIGHTS);

		writer.writeOpenTag(TreeModelParser.NODE_HEIGHTS,
				new Attribute[] {
						new Attribute.Default<String>(
								TreeModelParser.INTERNAL_NODES, "true"),
						new Attribute.Default<String>(
								TreeModelParser.ROOT_NODE, "true") });

		writeParameter(null, treeModelName + "." + "allInternalNodeHeights", 1,
				null, writer);

		writer.writeCloseTag(TreeModelParser.NODE_HEIGHTS);

		writer.writeCloseTag(TreeModel.TREE_MODEL);

	}
 

import dr.xml.XMLParser; //导入依赖的package包/类
@SuppressWarnings("rawtypes")
private void writeParameter(String wrapper, String id, int dimension,
		String value, XMLWriter writer) {

	if (wrapper != null) {
		writer.writeOpenTag(wrapper);
	}

	ArrayList<Attribute.Default> attributes = new ArrayList<Attribute.Default>();

	if (id != null) {
		attributes.add(new Attribute.Default<String>(XMLParser.ID, id));
	}

	if (dimension > 1) {
		attributes.add(new Attribute.Default<String>(
				ParameterParser.DIMENSION, String.valueOf(dimension)));
	}

	if (value != null) {
		attributes.add(new Attribute.Default<String>(ParameterParser.VALUE,
				value));
	}

	Attribute[] attrArray = new Attribute[attributes.size()];
	for (int i = 0; i < attrArray.length; i++) {
		attrArray[i] = attributes.get(i);
	}

	writer.writeTag(ParameterParser.PARAMETER, attrArray, true);

	if (wrapper != null) {
		writer.writeCloseTag(wrapper);
	}

}
 

import dr.xml.XMLParser; //导入依赖的package包/类
/**
 * Write the JC model XML block.
 *
 * @param num    the model number
 * @param writer the writer
 * @param model  the partition model to write in BEAST XML
 */
public void writeJCModel(int num, XMLWriter writer, PartitionSubstitutionModel model) {

    String prefix = model.getPrefix(num);

    writer.writeComment("The JC substitution model (Jukes & Cantor, 1969)");
    writer.writeOpenTag(NucModelType.HKY.getXMLName(),
            new Attribute[]{new Attribute.Default<String>(XMLParser.ID, prefix + "jc")}
    );
    writer.writeOpenTag(HKYParser.FREQUENCIES);
    writeFrequencyModelDNA(writer, model, num);
    writer.writeCloseTag(HKYParser.FREQUENCIES);

    writer.writeOpenTag(HKYParser.KAPPA);
    writeParameter("", 1, 1.0, Double.NaN, Double.NaN, writer);
    writer.writeCloseTag(HKYParser.KAPPA);

    writer.writeCloseTag(NucModelType.HKY.getXMLName());
}