Examples with SequenceErrorModelComponentOptions dr.app.beauti.components.sequenceerror.SequenceErrorModelComponentOptions used on opensource projects

Example 1 with SequenceErrorModelComponentOptions

use of dr.app.beauti.components.sequenceerror.SequenceErrorModelComponentOptions in project beast-mcmc by beast-dev.

the class PatternListGenerator method writePatternList.

/**
     * Writes the pattern lists
     *
     * @param partition the partition data to write the pattern lists for
     * @param writer    the writer
     */
public void writePatternList(PartitionData partition, XMLWriter writer) {
    writer.writeText("");
    AncestralStatesComponentOptions ancestralStatesOptions = (AncestralStatesComponentOptions) options.getComponentOptions(AncestralStatesComponentOptions.class);
    SequenceErrorModelComponentOptions sequenceErrorOptions = (SequenceErrorModelComponentOptions) options.getComponentOptions(SequenceErrorModelComponentOptions.class);
    PartitionSubstitutionModel model = partition.getPartitionSubstitutionModel();
    String codonHeteroPattern = model.getCodonHeteroPattern();
    int partitionCount = model.getCodonPartitionCount();
    boolean isAncestralStatesModel = (!ancestralStatesOptions.usingAncestralStates(partition) && !sequenceErrorOptions.usingSequenceErrorModel(partition));
    boolean isCovarionModel = model.getDataType().getType() == DataType.COVARION && model.getBinarySubstitutionModel() == BinaryModelType.BIN_COVARION;
    boolean unique = isAncestralStatesModel || isCovarionModel;
    boolean strip = isAncestralStatesModel || isCovarionModel;
    if (model.getDataType().getType() == DataType.NUCLEOTIDES && codonHeteroPattern != null && partitionCount > 1) {
        if (codonHeteroPattern.equals("112")) {
            writer.writeComment("The " + (unique ? "unique " : "") + "patterns for codon positions 1 & 2");
            writer.writeOpenTag(MergePatternsParser.MERGE_PATTERNS, new Attribute[] { new Attribute.Default<String>(XMLParser.ID, partition.getPrefix() + model.getPrefixCodon(1) + SitePatternsParser.PATTERNS) });
            writePatternList(partition, 0, 3, null, unique, strip, writer);
            writePatternList(partition, 1, 3, null, unique, strip, writer);
            writer.writeCloseTag(MergePatternsParser.MERGE_PATTERNS);
            writer.writeComment("The " + (unique ? "unique " : "") + "patterns for codon position 3");
            writePatternList(partition, 2, 3, model.getPrefixCodon(2), unique, strip, writer);
        } else {
            // pattern is 123
            for (int i = 1; i <= 3; i++) {
                writer.writeComment("The " + (unique ? "unique " : "") + "patterns for codon position " + i);
                writePatternList(partition, i - 1, 3, model.getPrefixCodon(i), unique, strip, writer);
            }
        }
    // END: pattern is 123
    } else {
        writePatternList(partition, 0, 1, "", unique, strip, writer);
    }
}