Examples with SequenceErrorType dr.app.beauti.types.SequenceErrorType used on opensource projects

Example 1 with SequenceErrorType

use of dr.app.beauti.types.SequenceErrorType in project beast-mcmc by beast-dev.

the class SequenceErrorModelComponentGenerator method generate.

protected void generate(final InsertionPoint point, final Object item, final String prefix, final XMLWriter writer) {
    SequenceErrorModelComponentOptions component = (SequenceErrorModelComponentOptions) options.getComponentOptions(SequenceErrorModelComponentOptions.class);
    switch(point) {
        case AFTER_PATTERNS:
            writeHypermutationAlignments(writer, component);
            break;
        case AFTER_SITE_MODEL:
            writeErrorModels(writer, component);
            break;
        case IN_TREE_LIKELIHOOD:
            AbstractPartitionData partition = (AbstractPartitionData) item;
            SequenceErrorType errorType = component.getSequenceErrorType(partition);
            if (errorType != SequenceErrorType.NO_ERROR) {
                writer.writeIDref(SequenceErrorModelParser.SEQUENCE_ERROR_MODEL, partition.getPrefix() + "errorModel");
            }
            break;
        case IN_FILE_LOG_PARAMETERS:
            writeLogParameters(writer, component);
            break;
        default:
            throw new IllegalArgumentException("This insertion point is not implemented for " + this.getClass().getName());
    }
}

Example 2 with SequenceErrorType

use of dr.app.beauti.types.SequenceErrorType in project beast-mcmc by beast-dev.

the class SequenceErrorModelComponentGenerator method writeLogParameters.

private void writeLogParameters(final XMLWriter writer, final SequenceErrorModelComponentOptions component) {
    for (AbstractPartitionData partition : options.getDataPartitions()) {
        //partition.getName() + ".";
        String prefix = partition.getPrefix();
        SequenceErrorType errorType = component.getSequenceErrorType(partition);
        if (errorType != SequenceErrorType.NO_ERROR) {
            if (component.isHypermutation(partition)) {
                writer.writeIDref(ParameterParser.PARAMETER, prefix + SequenceErrorModelComponentOptions.HYPERMUTION_RATE_PARAMETER);
                writer.writeIDref(StatisticParser.STATISTIC, prefix + SequenceErrorModelComponentOptions.HYPERMUTANT_COUNT_STATISTIC);
                writer.writeOpenTag(StatisticParser.STATISTIC, new Attribute.Default<String>("name", "isHypermutated"));
                writer.writeIDref(HypermutantErrorModel.HYPERMUTANT_ERROR_MODEL, prefix + SequenceErrorModelComponentOptions.ERROR_MODEL);
                writer.writeCloseTag(StatisticParser.STATISTIC);
            }
            if (component.hasAgeDependentRate(partition)) {
                writer.writeIDref(ParameterParser.PARAMETER, prefix + SequenceErrorModelComponentOptions.AGE_RATE_PARAMETER);
            }
            if (component.hasBaseRate(partition)) {
                writer.writeIDref(ParameterParser.PARAMETER, prefix + SequenceErrorModelComponentOptions.BASE_RATE_PARAMETER);
            }
        }
    }
}

Example 3 with SequenceErrorType

use of dr.app.beauti.types.SequenceErrorType in project beast-mcmc by beast-dev.

the class SequenceErrorModelComponentGenerator method writeHypermutationAlignments.

private void writeHypermutationAlignments(XMLWriter writer, SequenceErrorModelComponentOptions component) {
    for (AbstractPartitionData partition : options.getDataPartitions()) {
        //partition.getName() + ".";
        String prefix = partition.getPrefix();
        if (component.isHypermutation(partition)) {
            SequenceErrorType errorType = component.getSequenceErrorType(partition);
            final String errorTypeName;
            switch(errorType) {
                case HYPERMUTATION_ALL:
                    errorTypeName = HypermutantAlignment.APOBECType.ALL.toString();
                    break;
                case HYPERMUTATION_BOTH:
                    errorTypeName = HypermutantAlignment.APOBECType.BOTH.toString();
                    break;
                case HYPERMUTATION_HA3F:
                    errorTypeName = HypermutantAlignment.APOBECType.HA3F.toString();
                    break;
                case HYPERMUTATION_HA3G:
                    errorTypeName = HypermutantAlignment.APOBECType.HA3G.toString();
                    break;
                default:
                    throw new RuntimeException("Unknown ErrorModelType: " + errorType.toString());
            }
            writer.writeOpenTag(HypermutantAlignmentParser.HYPERMUTANT_ALIGNMENT, new Attribute[] { new Attribute.Default<String>(XMLParser.ID, prefix + "hypermutants"), new Attribute.Default<String>("type", errorTypeName) });
            writer.writeIDref("alignment", partition.getTaxonList().getId());
            writer.writeCloseTag(HypermutantAlignmentParser.HYPERMUTANT_ALIGNMENT);
        }
    }
}

Example 4 with SequenceErrorType

use of dr.app.beauti.types.SequenceErrorType in project beast-mcmc by beast-dev.

the class SequenceErrorModelComponentGenerator method writeErrorModels.

private void writeErrorModels(XMLWriter writer, SequenceErrorModelComponentOptions component) {
    for (AbstractPartitionData partition : options.getDataPartitions()) {
        //partition.getName() + ".";
        String prefix = partition.getPrefix();
        SequenceErrorType errorType = component.getSequenceErrorType(partition);
        if (component.isHypermutation(partition)) {
            writer.writeOpenTag(HypermutantErrorModel.HYPERMUTANT_ERROR_MODEL, new Attribute[] { new Attribute.Default<String>(XMLParser.ID, prefix + SequenceErrorModelComponentOptions.ERROR_MODEL) });
            writer.writeIDref(HypermutantAlignmentParser.HYPERMUTANT_ALIGNMENT, prefix + "hypermutants");
            writeParameter(HypermutantErrorModel.HYPERMUTATION_RATE, prefix + SequenceErrorModelComponentOptions.HYPERMUTION_RATE_PARAMETER, 1, writer);
            writeParameter(HypermutantErrorModel.HYPERMUTATION_INDICATORS, prefix + SequenceErrorModelComponentOptions.HYPERMUTANT_INDICATOR_PARAMETER, 1, writer);
            writer.writeCloseTag(HypermutantErrorModel.HYPERMUTANT_ERROR_MODEL);
            writer.writeOpenTag(SumStatisticParser.SUM_STATISTIC, new Attribute[] { new Attribute.Default<String>(XMLParser.ID, prefix + SequenceErrorModelComponentOptions.HYPERMUTANT_COUNT_STATISTIC), new Attribute.Default<Boolean>(SumStatisticParser.ELEMENTWISE, true) });
            writer.writeIDref(ParameterParser.PARAMETER, prefix + SequenceErrorModelComponentOptions.HYPERMUTANT_INDICATOR_PARAMETER);
            writer.writeCloseTag(SumStatisticParser.SUM_STATISTIC);
        } else if (errorType != SequenceErrorType.NO_ERROR) {
            final String errorTypeName = (errorType == SequenceErrorType.AGE_TRANSITIONS || errorType == SequenceErrorType.BASE_TRANSITIONS ? "transitions" : "all");
            writer.writeOpenTag(SequenceErrorModelParser.SEQUENCE_ERROR_MODEL, new Attribute[] { new Attribute.Default<String>(XMLParser.ID, prefix + SequenceErrorModelComponentOptions.ERROR_MODEL), new Attribute.Default<String>("type", errorTypeName) });
            if (component.hasAgeDependentRate(partition)) {
                writeParameter(SequenceErrorModelComponentOptions.AGE_RATE, prefix + SequenceErrorModelComponentOptions.AGE_RATE_PARAMETER, 1, writer);
            }
            if (component.hasBaseRate(partition)) {
                writeParameter(SequenceErrorModelComponentOptions.BASE_RATE, prefix + SequenceErrorModelComponentOptions.BASE_RATE_PARAMETER, 1, writer);
            }
            writer.writeCloseTag(SequenceErrorModelParser.SEQUENCE_ERROR_MODEL);
        }
    }
}

Example 5 with SequenceErrorType

use of dr.app.beauti.types.SequenceErrorType in project beast-mcmc by beast-dev.

the class SequenceErrorModelComponentOptions method getSequenceErrorType.

public SequenceErrorType getSequenceErrorType(final AbstractPartitionData partition) {
    SequenceErrorType type = sequenceErrorTypeMap.get(partition);
    if (type == null) {
        type = SequenceErrorType.NO_ERROR;
        sequenceErrorTypeMap.put(partition, type);
    }
    return type;
}