Examples with Attribute dr.util.Attribute used on opensource projects

Example 21 with Attribute

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

the class STARBEASTGenerator method writeStartingTreeForCalibration.

public void writeStartingTreeForCalibration(XMLWriter writer) {
    writer.writeComment("species starting tree for calibration");
    writer.writeText("");
    writer.writeOpenTag(OldCoalescentSimulatorParser.COALESCENT_TREE, new Attribute[] { new Attribute.Default<String>(XMLParser.ID, SP_START_TREE) });
    Attribute[] taxaAttribute = { new Attribute.Default<String>(XMLParser.IDREF, ALL_SPECIES) };
    writer.writeOpenTag(OldCoalescentSimulatorParser.CONSTRAINED_TAXA);
    writer.writeTag(TaxaParser.TAXA, taxaAttribute, true);
    for (Taxa taxa : options.speciesSets) {
        Parameter statistic = options.getStatistic(taxa);
        Attribute mono = new Attribute.Default<Boolean>(OldCoalescentSimulatorParser.IS_MONOPHYLETIC, options.speciesSetsMono.get(taxa));
        writer.writeOpenTag(OldCoalescentSimulatorParser.TMRCA_CONSTRAINT, mono);
        writer.writeIDref(TaxaParser.TAXA, taxa.getId());
        if (options.getPartitionTreePriors().get(0).getNodeHeightPrior() == TreePriorType.SPECIES_YULE_CALIBRATION && statistic.priorType == PriorType.UNIFORM_PRIOR) {
            writeDistribution(statistic, false, writer);
        }
        writer.writeCloseTag(OldCoalescentSimulatorParser.TMRCA_CONSTRAINT);
    }
    writer.writeCloseTag(OldCoalescentSimulatorParser.CONSTRAINED_TAXA);
    writer.writeOpenTag(ConstantPopulationModelParser.CONSTANT_POPULATION_MODEL, new Attribute[] { new Attribute.Default<String>(XMLParser.ID, "spInitDemo"), new Attribute.Default<String>("units", Units.Utils.getDefaultUnitName(options.units)) });
    writer.writeOpenTag(ConstantPopulationModelParser.POPULATION_SIZE);
    // "initial" is "value"
    double popSizeValue = options.getPartitionTreePriors().get(0).getParameter("constant.popSize").getInitial();
    writer.writeTag(ParameterParser.PARAMETER, new Attribute[] { new Attribute.Default<String>(XMLParser.ID, "sp.popSize"), new Attribute.Default<Double>(ParameterParser.VALUE, popSizeValue) }, true);
    writer.writeCloseTag(ConstantPopulationModelParser.POPULATION_SIZE);
    writer.writeCloseTag(ConstantPopulationModelParser.CONSTANT_POPULATION_MODEL);
    writer.writeCloseTag(OldCoalescentSimulatorParser.COALESCENT_TREE);
}

Example 22 with Attribute

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

the class STARBEASTGenerator method writeSpeciesTreePrior.

private void writeSpeciesTreePrior(XMLWriter writer) {
    Parameter para;
    TreePriorType nodeHeightPrior = options.getPartitionTreePriors().get(0).getNodeHeightPrior();
    if (nodeHeightPrior == TreePriorType.SPECIES_BIRTH_DEATH) {
        writer.writeComment("Species tree prior: Birth Death Model");
        writer.writeOpenTag(BirthDeathModelParser.BIRTH_DEATH_MODEL, new Attribute[] { new Attribute.Default<String>(XMLParser.ID, BirthDeathModelParser.BIRTH_DEATH), new Attribute.Default<String>(XMLUnits.UNITS, XMLUnits.SUBSTITUTIONS) });
        writer.writeOpenTag(BirthDeathModelParser.BIRTHDIFF_RATE);
        para = options.starBEASTOptions.getParameter(TraitData.TRAIT_SPECIES + "." + BirthDeathModelParser.MEAN_GROWTH_RATE_PARAM_NAME);
        //            writer.writeTag(ParameterParser.PARAMETER, new Attribute[]{
        //                    new Attribute.Default<String>(XMLParser.ID, TraitData.TRAIT_SPECIES + "." + BirthDeathModelParser.MEAN_GROWTH_RATE_PARAM_NAME),
        //                    new Attribute.Default<String>(ParameterParser.VALUE, Double.toString(para.initial)),
        //                    new Attribute.Default<String>(ParameterParser.LOWER, Double.toString(para.lower)),
        //                    new Attribute.Default<String>(ParameterParser.UPPER, Double.toString(para.upper))}, true);
        writeParameter(TraitData.TRAIT_SPECIES + "." + BirthDeathModelParser.MEAN_GROWTH_RATE_PARAM_NAME, para, writer);
        writer.writeCloseTag(BirthDeathModelParser.BIRTHDIFF_RATE);
        writer.writeOpenTag(BirthDeathModelParser.RELATIVE_DEATH_RATE);
        para = options.starBEASTOptions.getParameter(TraitData.TRAIT_SPECIES + "." + BirthDeathModelParser.RELATIVE_DEATH_RATE_PARAM_NAME);
        //            writer.writeTag(ParameterParser.PARAMETER, new Attribute[]{
        //                    new Attribute.Default<String>(XMLParser.ID, TraitData.TRAIT_SPECIES + "." + BirthDeathModelParser.RELATIVE_DEATH_RATE_PARAM_NAME),
        //                    new Attribute.Default<String>(ParameterParser.VALUE, Double.toString(para.initial)),
        //                    new Attribute.Default<String>(ParameterParser.LOWER, Double.toString(para.lower)),
        //                    new Attribute.Default<String>(ParameterParser.UPPER, Double.toString(para.upper))}, true);
        writeParameter(TraitData.TRAIT_SPECIES + "." + BirthDeathModelParser.RELATIVE_DEATH_RATE_PARAM_NAME, para, writer);
        writer.writeCloseTag(BirthDeathModelParser.RELATIVE_DEATH_RATE);
        writer.writeCloseTag(BirthDeathModelParser.BIRTH_DEATH_MODEL);
    } else if (nodeHeightPrior == TreePriorType.SPECIES_YULE || nodeHeightPrior == TreePriorType.SPECIES_YULE_CALIBRATION) {
        writer.writeComment("Species tree prior: Yule Model");
        writer.writeOpenTag(YuleModelParser.YULE_MODEL, new Attribute[] { new Attribute.Default<String>(XMLParser.ID, YuleModelParser.YULE), new Attribute.Default<String>(XMLUnits.UNITS, XMLUnits.SUBSTITUTIONS) });
        writer.writeOpenTag(YuleModelParser.BIRTH_RATE);
        para = options.starBEASTOptions.getParameter(TraitData.TRAIT_SPECIES + "." + YuleModelParser.YULE + "." + YuleModelParser.BIRTH_RATE);
        //            writer.writeTag(ParameterParser.PARAMETER, new Attribute[]{
        //                    new Attribute.Default<String>(XMLParser.ID, TraitData.TRAIT_SPECIES + "." + YuleModelParser.YULE + "." + YuleModelParser.BIRTH_RATE),
        //                    new Attribute.Default<String>(ParameterParser.VALUE, Double.toString(para.initial)),
        //                    new Attribute.Default<String>(ParameterParser.LOWER, Double.toString(para.lower)),
        //                    new Attribute.Default<String>(ParameterParser.UPPER, Double.toString(para.upper))}, true);
        writeParameter(TraitData.TRAIT_SPECIES + "." + YuleModelParser.YULE + "." + YuleModelParser.BIRTH_RATE, para, writer);
        writer.writeCloseTag(YuleModelParser.BIRTH_RATE);
        writer.writeCloseTag(YuleModelParser.YULE_MODEL);
    } else if (nodeHeightPrior == TreePriorType.SPECIES_YULE_CALIBRATION) {
    } else {
        throw new IllegalArgumentException("Get wrong species tree prior using *BEAST : " + nodeHeightPrior.toString());
    }
}

Example 23 with Attribute

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

the class XMLWriter method writeTag.

public void writeTag(String tagname, Attribute[] attributes, boolean close) {
    StringBuffer buffer = new StringBuffer("<");
    buffer.append(tagname);
    for (Attribute attribute : attributes) {
        if (attribute != null) {
            buffer.append(' ');
            buffer.append(attribute.getAttributeName());
            buffer.append("=\"");
            buffer.append(attribute.getAttributeValue());
            buffer.append("\"");
        }
    }
    if (close) {
        buffer.append("/");
    }
    buffer.append(">");
    writeText(buffer.toString());
    if (!close) {
        increaseLevel();
    }
}

Example 24 with Attribute

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

the class SubstitutionModelGenerator method writeSubstitutionSiteModel.

/**
     * Writes the substitution model to XML.
     *
     * @param writer the writer
     * @param model  the partition model to write in BEAST XML
     */
public void writeSubstitutionSiteModel(PartitionSubstitutionModel model, XMLWriter writer) {
    DataType dataType = model.getDataType();
    String dataTypeDescription = dataType.getDescription();
    switch(dataType.getType()) {
        case DataType.NUCLEOTIDES:
            if (model.isUnlinkedSubstitutionModel()) {
                for (int i = 1; i <= model.getCodonPartitionCount(); i++) {
                    switch(model.getNucSubstitutionModel()) {
                        case JC:
                            writeJCModel(i, writer, model);
                            break;
                        case HKY:
                            writeHKYModel(i, writer, model);
                            break;
                        case TN93:
                            writeTN93Model(i, writer, model);
                            break;
                        case GTR:
                            writeGTRModel(i, writer, model);
                            break;
                        default:
                            throw new IllegalArgumentException("unknown substition model type");
                    }
                }
            } else {
                switch(model.getNucSubstitutionModel()) {
                    case JC:
                        writeJCModel(-1, writer, model);
                        break;
                    case HKY:
                        writeHKYModel(-1, writer, model);
                        break;
                    case TN93:
                        writeTN93Model(-1, writer, model);
                        break;
                    case GTR:
                        writeGTRModel(-1, writer, model);
                        break;
                    default:
                        throw new IllegalArgumentException("unknown substitution model type");
                }
            }
            //****************** Site Model *****************
            if (model.getCodonPartitionCount() > 1) {
                //model.getCodonHeteroPattern() != null) {
                for (int i = 1; i <= model.getCodonPartitionCount(); i++) {
                    writeNucSiteModel(i, writer, model);
                }
                writer.println();
            } else {
                writeNucSiteModel(-1, writer, model);
            }
            break;
        case DataType.AMINO_ACIDS:
            // Amino Acid model
            String aaModel = model.getAaSubstitutionModel().getXMLName();
            writer.writeComment("The " + aaModel + " substitution model");
            writer.writeTag(EmpiricalAminoAcidModelParser.EMPIRICAL_AMINO_ACID_MODEL, new Attribute[] { new Attribute.Default<String>(XMLParser.ID, model.getPrefix() + "aa"), new Attribute.Default<String>("type", aaModel) }, true);
            //****************** Site Model *****************
            writeAASiteModel(writer, model);
            break;
        case DataType.TWO_STATES:
        case DataType.COVARION:
            switch(model.getBinarySubstitutionModel()) {
                case BIN_DOLLO:
                    return;
                case BIN_SIMPLE:
                    writeBinarySimpleModel(writer, model);
                    break;
                case BIN_COVARION:
                    writeBinaryCovarionModel(writer, model);
                    break;
            }
            //****************** Site Model *****************
            writeTwoStateSiteModel(writer, model);
            break;
        case DataType.GENERAL:
        case DataType.CONTINUOUS:
            //handled by component
            break;
        case DataType.MICRO_SAT:
            writeMicrosatSubstModel(model, writer);
            break;
        default:
            throw new IllegalArgumentException("Unknown data type");
    }
}

Example 25 with Attribute

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

the class TreeModelGenerator method writeTreeModel.

/**
     * Write tree model XML block.
     *
     * @param model
     * @param writer the writer
     */
void writeTreeModel(PartitionTreeModel model, XMLWriter writer) {
    setModelPrefix(model.getPrefix());
    // treemodel.treeModel or treeModel
    final String treeModelName = modelPrefix + TreeModel.TREE_MODEL;
    writer.writeComment("Generate a tree model");
    writer.writeTag(TreeModel.TREE_MODEL, new Attribute.Default<String>(XMLParser.ID, treeModelName), false);
    final String STARTING_TREE = InitialTreeGenerator.STARTING_TREE;
    switch(model.getStartingTreeType()) {
        case USER:
            writer.writeIDref("tree", modelPrefix + STARTING_TREE);
            break;
        case UPGMA:
            writer.writeIDref(UPGMATreeParser.UPGMA_TREE, modelPrefix + STARTING_TREE);
            break;
        case RANDOM:
            writer.writeIDref(OldCoalescentSimulatorParser.COALESCENT_TREE, modelPrefix + STARTING_TREE);
            break;
        default:
            throw new IllegalArgumentException("Unknown StartingTreeType");
    }
    writer.writeOpenTag(TreeModelParser.ROOT_HEIGHT);
    writer.writeTag(ParameterParser.PARAMETER, new Attribute.Default<String>(XMLParser.ID, treeModelName + "." + OldCoalescentSimulatorParser.ROOT_HEIGHT), true);
    writer.writeCloseTag(TreeModelParser.ROOT_HEIGHT);
    writer.writeOpenTag(TreeModelParser.NODE_HEIGHTS, new Attribute.Default<String>(TreeModelParser.INTERNAL_NODES, "true"));
    writer.writeTag(ParameterParser.PARAMETER, new Attribute.Default<String>(XMLParser.ID, treeModelName + "." + "internalNodeHeights"), true);
    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") });
    writer.writeTag(ParameterParser.PARAMETER, new Attribute.Default<String>(XMLParser.ID, treeModelName + "." + "allInternalNodeHeights"), true);
    writer.writeCloseTag(TreeModelParser.NODE_HEIGHTS);
    //        int randomLocalClockCount = 0;
    //        int autocorrelatedClockCount = 0;
    //        for (PartitionData pd : model.getDataPartitions()) { // only the PDs linked to this tree model
    //        	PartitionClockModel clockModel = pd.getPartitionClockModel();
    //        	switch (clockModel.getClockType()) {
    //	        	case AUTOCORRELATED_LOGNORMAL: autocorrelatedClockCount += 1; break;
    //	        	case RANDOM_LOCAL_CLOCK: randomLocalClockCount += 1; break;
    //        	}
    //        }
    //
    //        if (autocorrelatedClockCount > 1 || randomLocalClockCount > 1 || autocorrelatedClockCount + randomLocalClockCount > 1) {
    //        	//FAIL
    //            throw new IllegalArgumentException("clock model/tree model combination not implemented by BEAST yet!");
    //        }
    // move to validateClockTreeModelCombination(PartitionTreeModel model)
    //    	if (autocorrelatedClockCount == 1) {
    //        if (count[0] == 1) {
    //                writer.writeOpenTag(TreeModelParser.NODE_RATES,
    //                        new Attribute[]{
    //                                new Attribute.Default<String>(TreeModelParser.ROOT_NODE, "false"),
    //                                new Attribute.Default<String>(TreeModelParser.INTERNAL_NODES, "true"),
    //                                new Attribute.Default<String>(TreeModelParser.LEAF_NODES, "true")
    //                        });
    //                writer.writeTag(ParameterParser.PARAMETER,
    //                        new Attribute.Default<String>(XMLParser.ID, treeModelName + "." + TreeModelParser.NODE_RATES), true);
    //                writer.writeCloseTag(TreeModelParser.NODE_RATES);
    //
    //                writer.writeOpenTag(TreeModelParser.NODE_RATES,
    //                        new Attribute[]{
    //                                new Attribute.Default<String>(TreeModelParser.ROOT_NODE, "true"),
    //                                new Attribute.Default<String>(TreeModelParser.INTERNAL_NODES, "false"),
    //                                new Attribute.Default<String>(TreeModelParser.LEAF_NODES, "false")
    //                        });
    //                writer.writeTag(ParameterParser.PARAMETER,
    //                        new Attribute.Default<String>(XMLParser.ID,
    //                                treeModelName + "." + RateEvolutionLikelihood.ROOTRATE), true);
    //                writer.writeCloseTag(TreeModelParser.NODE_RATES);
    ////    	} else if (randomLocalClockCount == 1 ) {
    //        } else
    //+++++++++++++ removed because random local clock XML is changed ++++++++++++++++
    //        int[] count = validateClockTreeModelCombination(model);
    //        if (count[1] == 1) {
    //            writer.writeOpenTag(TreeModelParser.NODE_RATES,
    //                    new Attribute[]{
    //                            new Attribute.Default<String>(TreeModelParser.ROOT_NODE, "false"),
    //                            new Attribute.Default<String>(TreeModelParser.INTERNAL_NODES, "true"),
    //                            new Attribute.Default<String>(TreeModelParser.LEAF_NODES, "true")
    //                    });
    //            writer.writeTag(ParameterParser.PARAMETER,
    //                    new Attribute.Default<String>(XMLParser.ID, modelPrefix + ClockType.LOCAL_CLOCK + ".relativeRates"), true);
    //            writer.writeCloseTag(TreeModelParser.NODE_RATES);
    //
    //            writer.writeOpenTag(TreeModelParser.NODE_TRAITS,
    //                    new Attribute[]{
    //                            new Attribute.Default<String>(TreeModelParser.ROOT_NODE, "false"),
    //                            new Attribute.Default<String>(TreeModelParser.INTERNAL_NODES, "true"),
    //                            new Attribute.Default<String>(TreeModelParser.LEAF_NODES, "true")
    //                    });
    //            writer.writeTag(ParameterParser.PARAMETER,
    //                    new Attribute.Default<String>(XMLParser.ID, modelPrefix + ClockType.LOCAL_CLOCK + ".changes"), true);
    //            writer.writeCloseTag(TreeModelParser.NODE_TRAITS);
    //        }
    generateInsertionPoint(ComponentGenerator.InsertionPoint.IN_TREE_MODEL, model, writer);
    writer.writeCloseTag(TreeModel.TREE_MODEL);
    //        if (autocorrelatedClockCount == 1) {
    //        if (count[0] == 1) {
    //            writer.writeText("");
    //            writer.writeOpenTag(CompoundParameter.COMPOUND_PARAMETER,
    //                    new Attribute[]{new Attribute.Default<String>(XMLParser.ID, treeModelName + "." + "allRates")});
    //            writer.writeIDref(ParameterParser.PARAMETER, treeModelName + "." + TreeModelParser.NODE_RATES);
    //            writer.writeIDref(ParameterParser.PARAMETER, treeModelName + "." + RateEvolutionLikelihood.ROOTRATE);
    //            writer.writeCloseTag(CompoundParameter.COMPOUND_PARAMETER);
    //        }
    writer.writeComment("Statistic for time of most recent common ancestor of tree");
    writer.writeTag(TMRCAStatisticParser.TMRCA_STATISTIC, new Attribute[] { new Attribute.Default<String>(XMLParser.ID, treeModelName + ".rootAge"), new Attribute.Default<String>(TMRCAStatisticParser.ABSOLUTE, "true") }, false);
    writer.writeIDref(TreeModel.TREE_MODEL, treeModelName);
    writer.writeCloseTag(TMRCAStatisticParser.TMRCA_STATISTIC);
    if (model.getDataType().getType() == DataType.MICRO_SAT) {
        for (AbstractPartitionData partitionData : options.getDataPartitions(model)) {
            writer.writeComment("Generate a microsatellite tree model");
            writer.writeTag(MicrosatelliteSamplerTreeModelParser.TREE_MICROSATELLITE_SAMPLER_MODEL, new Attribute.Default<String>(XMLParser.ID, partitionData.getName() + "." + MicrosatelliteSamplerTreeModelParser.TREE_MICROSATELLITE_SAMPLER_MODEL), false);
            writer.writeOpenTag(MicrosatelliteSamplerTreeModelParser.TREE);
            writer.writeIDref(TreeModel.TREE_MODEL, treeModelName);
            writer.writeCloseTag(MicrosatelliteSamplerTreeModelParser.TREE);
            writer.writeOpenTag(MicrosatelliteSamplerTreeModelParser.INTERNAL_VALUES);
            writer.writeTag(ParameterParser.PARAMETER, new Attribute[] { new Attribute.Default<String>(XMLParser.ID, partitionData.getName() + "." + MicrosatelliteSamplerTreeModelParser.TREE_MICROSATELLITE_SAMPLER_MODEL + ".internalNodesParameter"), new Attribute.Default<Integer>(ParameterParser.DIMENSION, model.getDimension()) }, true);
            writer.writeCloseTag(MicrosatelliteSamplerTreeModelParser.INTERNAL_VALUES);
            writer.writeOpenTag(MicrosatelliteSamplerTreeModelParser.EXTERNAL_VALUES);
            writer.writeIDref(MicrosatellitePatternParser.MICROSATPATTERN, partitionData.getName());
            writer.writeCloseTag(MicrosatelliteSamplerTreeModelParser.EXTERNAL_VALUES);
            writer.writeCloseTag(MicrosatelliteSamplerTreeModelParser.TREE_MICROSATELLITE_SAMPLER_MODEL);
        }
    }
}