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

Example 11 with Attribute

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

the class InitialTreeGenerator method writeStartingTree.

/**
     * Generate XML for the starting tree
     * @param model  PartitionTreeModel
     *
     * @param writer the writer
     */
public void writeStartingTree(PartitionTreeModel model, XMLWriter writer) {
    // only has prefix, if (options.getPartitionTreeModels().size() > 1)
    setModelPrefix(model.getPrefix());
    switch(model.getStartingTreeType()) {
        case USER:
        case UPGMA:
            Parameter rootHeight = model.getParameter("treeModel.rootHeight");
            // generate a rescaled starting tree
            writer.writeComment("Construct a starting tree that is compatible with specified clade heights");
            Attribute[] attributes = (rootHeight.priorType != PriorType.NONE_TREE_PRIOR ? new Attribute[] { new Attribute.Default<String>(XMLParser.ID, modelPrefix + STARTING_TREE), new Attribute.Default<String>(RescaledTreeParser.HEIGHT, "" + rootHeight.getInitial()) } : new Attribute[] { new Attribute.Default<String>(XMLParser.ID, modelPrefix + STARTING_TREE) });
            writer.writeOpenTag(RescaledTreeParser.RESCALED_TREE, attributes);
            writeSourceTree(model, writer);
            if (options.taxonSets != null && options.taxonSets.size() > 0 && !options.useStarBEAST) {
                for (Taxa taxa : options.taxonSets) {
                    Double height = options.taxonSetsHeights.get(taxa);
                    if (height != null) {
                        writer.writeOpenTag(RescaledTreeParser.CLADE, new Attribute.Default<String>(RescaledTreeParser.HEIGHT, height.toString()));
                        writer.writeTag("taxa", new Attribute.Default<String>(XMLParser.IDREF, taxa.getId()), true);
                        writer.writeCloseTag(RescaledTreeParser.CLADE);
                    } else if (options.taxonSetsMono.get(taxa)) {
                        // if monophyly is enforced then placing this clade element here will force BEAST to check
                        // the clade exists in the tree.
                        writer.writeOpenTag(RescaledTreeParser.CLADE);
                        writer.writeTag("taxa", new Attribute.Default<String>(XMLParser.IDREF, taxa.getId()), true);
                        writer.writeCloseTag(RescaledTreeParser.CLADE);
                    }
                }
            }
            writer.writeCloseTag(RescaledTreeParser.RESCALED_TREE);
            break;
        case RANDOM:
            // generate a coalescent tree
            String simulatorId = modelPrefix + STARTING_TREE;
            String taxaId = TaxaParser.TAXA;
            AbstractPartitionData partition = options.getDataPartitions(model).get(0);
            if (!options.hasIdenticalTaxa()) {
                taxaId = partition.getPartitionTreeModel().getPrefix() + TaxaParser.TAXA;
            }
            if (partition instanceof PartitionPattern && ((PartitionPattern) partition).getPatterns().hasMask()) {
                taxaId = partition.getPrefix() + TaxaParser.TAXA;
            }
            writer.writeComment("Generate a random starting tree under the coalescent process");
            if (options.taxonSets != null && options.taxonSets.size() > 0 && !options.useStarBEAST) {
                // need !options.useStarBEAST,
                writeSubTree(simulatorId, taxaId, options.taxonList, model, writer);
            } else {
                writer.writeOpenTag(CoalescentSimulatorParser.COALESCENT_SIMULATOR, new Attribute[] { new Attribute.Default<String>(XMLParser.ID, simulatorId) });
                writeTaxaRef(taxaId, model, writer);
                writeInitialDemoModelRef(model, writer);
                writer.writeCloseTag(CoalescentSimulatorParser.COALESCENT_SIMULATOR);
            }
            break;
        default:
            throw new IllegalArgumentException("Unknown StartingTreeType");
    }
}

Example 12 with Attribute

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

the class InitialTreeGenerator method writeTaxaRef.

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);
    }
}

Example 13 with Attribute

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

the class LogGenerator method writeDemographicLogToFile.

public void writeDemographicLogToFile(XMLWriter writer, TreePriorGenerator treePriorGenerator, ClockModelGenerator clockModelGenerator, SubstitutionModelGenerator substitutionModelGenerator, TreeLikelihoodGenerator treeLikelihoodGenerator) {
    writer.writeComment("demographic log file");
    if (options.demographicLogFileName == null) {
        options.demographicLogFileName = options.fileNameStem + ".demo.log";
    }
    String header = "Demographic Model: " + options.demographicModelName;
    writer.writeOpenTag(LoggerParser.LOG, new Attribute[] { new Attribute.Default<String>(XMLParser.ID, "fileLog"), new Attribute.Default<String>(LoggerParser.HEADER, header + ""), new Attribute.Default<String>(LoggerParser.LOG_EVERY, options.logEvery + ""), new Attribute.Default<String>(LoggerParser.FILE_NAME, options.logFileName), new Attribute.Default<Boolean>(LoggerParser.ALLOW_OVERWRITE_LOG, options.allowOverwriteLog) });
    if (options.hasData()) {
        writer.writeIDref(CompoundLikelihoodParser.POSTERIOR, "posterior");
    }
    writer.writeIDref(CompoundLikelihoodParser.PRIOR, "prior");
    for (PartitionTreeModel model : options.getPartitionTreeModels()) {
        writer.writeIDref(ParameterParser.PARAMETER, model.getPrefix() + TreeModel.TREE_MODEL + "." + TreeModelParser.ROOT_HEIGHT);
    }
    if (options.useStarBEAST) {
        for (Taxa taxa : options.speciesSets) {
            // make tmrca(tree.name) eay to read in log for Tracer
            writer.writeIDref(TMRCAStatisticParser.TMRCA_STATISTIC, "tmrca(" + taxa.getId() + ")");
        }
    } else {
        for (Taxa taxa : options.taxonSets) {
            // make tmrca(tree.name) eay to read in log for Tracer
            PartitionTreeModel treeModel = options.taxonSetsTreeModel.get(taxa);
            writer.writeIDref(TMRCAStatisticParser.TMRCA_STATISTIC, "tmrca(" + treeModel.getPrefix() + taxa.getId() + ")");
        }
    }
    //        } else { // no species
    for (PartitionTreePrior prior : options.getPartitionTreePriors()) {
        //	        	treePriorGenerator.setModelPrefix(prior.getPrefix()); // priorName.treeModel
        treePriorGenerator.writeParameterLog(prior, writer);
    }
    for (PartitionSubstitutionModel model : options.getPartitionSubstitutionModels()) {
        substitutionModelGenerator.writeLog(model, writer);
    }
    for (PartitionClockModel model : options.getPartitionClockModels()) {
        //            if (model.getRateTypeOption() == FixRateType.FIXED_MEAN) {
        //                writer.writeIDref(ParameterParser.PARAMETER, model.getName());
        //                if (model.getClockType() == ClockType.UNCORRELATED) {
        //                    switch (model.getClockDistributionType()) {
        //                        case LOGNORMAL:
        //                            writer.writeIDref(ParameterParser.PARAMETER, model.getPrefix() + ClockType.UCLD_STDEV);
        //                            break;
        //                        case GAMMA:
        //                            throw new UnsupportedOperationException("Uncorrelated gamma model not implemented yet");
        ////                            break;
        //                        case CAUCHY:
        //                            throw new UnsupportedOperationException("Uncorrelated Cauchy model not implemented yet");
        ////                            break;
        //                        case EXPONENTIAL:
        //                            // nothing required
        //                            break;
        //                    }
        //                }
        //            }
        clockModelGenerator.writeLog(model, writer);
    }
    for (PartitionClockModel model : options.getPartitionClockModels()) {
        clockModelGenerator.writeLogStatistic(model, writer);
    }
    generateInsertionPoint(ComponentGenerator.InsertionPoint.IN_FILE_LOG_PARAMETERS, writer);
    treeLikelihoodGenerator.writeTreeLikelihoodReferences(writer);
    clockModelGenerator.writeClockLikelihoodReferences(writer);
    generateInsertionPoint(ComponentGenerator.InsertionPoint.IN_FILE_LOG_LIKELIHOODS, writer);
    // coalescentLikelihood
    for (PartitionTreeModel model : options.getPartitionTreeModels()) {
        PartitionTreePrior prior = model.getPartitionTreePrior();
        treePriorGenerator.writePriorLikelihoodReferenceLog(prior, model, writer);
        writer.writeText("");
    }
    for (PartitionTreePrior prior : options.getPartitionTreePriors()) {
        if (prior.getNodeHeightPrior() == TreePriorType.EXTENDED_SKYLINE) {
            // only 1 coalescent
            writer.writeIDref(CoalescentLikelihoodParser.COALESCENT_LIKELIHOOD, prior.getPrefix() + COALESCENT);
        } else if (prior.getNodeHeightPrior() == TreePriorType.SKYGRID) {
            writer.writeIDref(GMRFSkyrideLikelihoodParser.SKYGRID_LIKELIHOOD, prior.getPrefix() + "skygrid");
        }
    }
    writer.writeCloseTag(LoggerParser.LOG);
    generateInsertionPoint(ComponentGenerator.InsertionPoint.AFTER_FILE_LOG, writer);
}

Example 14 with Attribute

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

the class OperatorsGenerator method writeOperatorSchedule.

/**
     * Write the operator schedule XML block.
     *
     * @param operators the list of operators
     * @param writer    the writer
     */
public void writeOperatorSchedule(List<Operator> operators, XMLWriter writer) {
    Attribute[] operatorAttributes;
    // certain models would benefit from a logarithm operator optimization
    boolean shouldLogCool = false;
    for (PartitionTreePrior partition : options.getPartitionTreePriors()) {
        if (partition.getNodeHeightPrior() == TreePriorType.SKYGRID || partition.getNodeHeightPrior() == TreePriorType.GMRF_SKYRIDE) {
            shouldLogCool = true;
            break;
        }
    }
    for (PartitionSubstitutionModel model : options.getPartitionSubstitutionModels()) {
        if (model.getDataType().getType() == DataType.GENERAL || model.getDataType().getType() == DataType.CONTINUOUS) {
            shouldLogCool = true;
            break;
        }
    }
    operatorAttributes = new Attribute[] { new Attribute.Default<String>(XMLParser.ID, "operators"), new Attribute.Default<String>(SimpleOperatorScheduleParser.OPTIMIZATION_SCHEDULE, (shouldLogCool ? OperatorSchedule.OptimizationTransform.LOG.toString() : OperatorSchedule.OptimizationTransform.DEFAULT.toString())) };
    writer.writeComment("Define operators");
    writer.writeOpenTag(SimpleOperatorScheduleParser.OPERATOR_SCHEDULE, operatorAttributes);
    for (Operator operator : operators) {
        if (operator.getWeight() > 0. && operator.isUsed()) {
            setModelPrefix(operator.getPrefix());
            writeOperator(operator, writer);
        }
    }
    // Added for special operators
    generateInsertionPoint(ComponentGenerator.InsertionPoint.IN_OPERATORS, writer);
    writer.writeCloseTag(SimpleOperatorScheduleParser.OPERATOR_SCHEDULE);
}

Example 15 with Attribute

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

the class PatternListGenerator method writePatternList.

/**
     * Micro-sat
     * @param partition
     * @param microsatList
     * @param writer
     */
public void writePatternList(PartitionPattern partition, List<Microsatellite> microsatList, XMLWriter writer) throws GeneratorException {
    PartitionSubstitutionModel model = partition.getPartitionSubstitutionModel();
    if (model.getDataType().getType() == DataType.MICRO_SAT) {
        Patterns patterns = partition.getPatterns();
        writer.writeComment("The patterns for microsatellite");
        writer.writeOpenTag(MicrosatellitePatternParser.MICROSATPATTERN, new Attribute[] { new Attribute.Default<String>(XMLParser.ID, partition.getName()) });
        if (options.hasIdenticalTaxa() && !patterns.hasMask()) {
            writer.writeIDref(TaxaParser.TAXA, TaxaParser.TAXA);
        } else {
            writer.writeIDref(TaxaParser.TAXA, partition.getName() + "." + TaxaParser.TAXA);
        }
        Microsatellite m = model.getMicrosatellite();
        if (m == null)
            throw new GeneratorException("Microsatellite is null in partition:\n" + partition.getName());
        if (!microsatList.contains(m)) {
            microsatList.add(m);
            writer.writeTag(MicrosatelliteParser.MICROSAT, new Attribute[] { new Attribute.Default<String>(XMLParser.ID, m.getName()), new Attribute.Default<Integer>(MicrosatelliteParser.MAX, m.getMax()), new Attribute.Default<Integer>(MicrosatelliteParser.MIN, m.getMin()), new Attribute.Default<Integer>(MicrosatelliteParser.UNIT_LENGTH, m.getUnitLength()) }, true);
        } else {
            writer.writeTag(MicrosatelliteParser.MICROSAT, new Attribute[] { new Attribute.Default<String>(XMLParser.IDREF, m.getName()) }, true);
        }
        writer.writeOpenTag(MicrosatellitePatternParser.MICROSAT_SEQ);
        String seq = "";
        int c = 0;
        for (int i = 0; i < patterns.getTaxonCount(); i++) {
            if (!patterns.isMasked(i)) {
                if (c > 0)
                    seq += ",";
                int state = patterns.getPatternState(i, 0);
                if (state == Microsatellite.UNKNOWN_STATE_LENGTH) {
                    seq += Microsatellite.UNKNOWN_CHARACTER;
                } else {
                    seq += Integer.toString(state);
                }
                c++;
            }
        }
        writer.writeText(seq);
        writer.writeCloseTag(MicrosatellitePatternParser.MICROSAT_SEQ);
        writer.writeCloseTag(MicrosatellitePatternParser.MICROSATPATTERN);
    } else {
    }
}