Examples with Alignment dr.evolution.alignment.Alignment used on opensource projects

Example 11 with Alignment

use of dr.evolution.alignment.Alignment in project beast-mcmc by beast-dev.

the class SitePatternsParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Alignment alignment = (Alignment) xo.getChild(Alignment.class);
    TaxonList taxa = null;
    int from = 0;
    int to = -1;
    int every = xo.getAttribute(EVERY, 1);
    boolean strip = xo.getAttribute(STRIP, true);
    boolean unique = xo.getAttribute(UNIQUE, true);
    if (xo.hasAttribute(FROM)) {
        from = xo.getIntegerAttribute(FROM) - 1;
        if (from < 0)
            throw new XMLParseException("illegal 'from' attribute in patterns element");
    }
    if (xo.hasAttribute(TO)) {
        to = xo.getIntegerAttribute(TO) - 1;
        if (to < 0 || to < from)
            throw new XMLParseException("illegal 'to' attribute in patterns element");
    }
    if (every <= 0)
        throw new XMLParseException("illegal 'every' attribute in patterns element");
    if (xo.hasChildNamed(TAXON_LIST)) {
        taxa = (TaxonList) xo.getElementFirstChild(TAXON_LIST);
    }
    int[] constantPatternCounts = null;
    if (xo.hasChildNamed(CONSTANT_PATTERNS)) {
        Parameter param = (Parameter) xo.getElementFirstChild(CONSTANT_PATTERNS);
        if (param.getDimension() != alignment.getStateCount()) {
            throw new XMLParseException("The " + CONSTANT_PATTERNS + " parameter length should be equal to the number of states");
        }
        constantPatternCounts = new int[param.getDimension()];
        int i = 0;
        for (double value : param.getParameterValues()) {
            constantPatternCounts[i] = (int) value;
            i++;
        }
    }
    if (from > alignment.getSiteCount())
        throw new XMLParseException("illegal 'from' attribute in patterns element");
    if (to > alignment.getSiteCount())
        throw new XMLParseException("illegal 'to' attribute in patterns element");
    SitePatterns patterns = new SitePatterns(alignment, taxa, from, to, every, strip, unique, constantPatternCounts);
    int f = from + 1;
    // fixed a *display* error by adding + 1 for consistency with f = from + 1
    int t = to + 1;
    if (to == -1)
        t = alignment.getSiteCount();
    if (xo.hasAttribute(XMLParser.ID)) {
        final Logger logger = Logger.getLogger("dr.evoxml");
        logger.info("Site patterns '" + xo.getId() + "' created from positions " + Integer.toString(f) + "-" + Integer.toString(t) + " of alignment '" + alignment.getId() + "'");
        if (every > 1) {
            logger.info("  only using every " + every + " site");
        }
        logger.info("  " + (unique ? "unique " : "") + "pattern count = " + patterns.getPatternCount());
    }
    return patterns;
}

Example 12 with Alignment

use of dr.evolution.alignment.Alignment in project beast-mcmc by beast-dev.

the class HypermutantAlignmentParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Alignment alignment = (Alignment) xo.getChild(Alignment.class);
    if (alignment.getDataType().getType() != DataType.NUCLEOTIDES) {
        throw new XMLParseException("HypermutantAlignment can only convert nucleotide alignments");
    }
    String typeName = xo.getStringAttribute(CONTEXT_TYPE);
    HypermutantAlignment.APOBECType type = null;
    try {
        type = HypermutantAlignment.APOBECType.valueOf(typeName.toUpperCase());
    } catch (IllegalArgumentException iae) {
        throw new XMLParseException("Unrecognised hypermutation type: " + typeName);
    }
    HypermutantAlignment convert = new HypermutantAlignment(type, alignment);
    int mutatedCount = convert.getMutatedContextCount();
    int totalCount = mutatedCount + convert.getUnmutatedContextCount();
    Logger.getLogger("dr.evoxml").info("Converted alignment, '" + xo.getId() + "' to a hypermutant alignment targeting " + type.toString() + " contexts.\r" + "\tPotentially mutated contexts: " + mutatedCount + " out of a total of " + totalCount + " contexts");
    return convert;
}

Example 13 with Alignment

use of dr.evolution.alignment.Alignment in project beast-mcmc by beast-dev.

the class MetagenomeDataParser method parseXMLObject.

@Override
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    TaxonList taxa = null;
    taxa = (TaxonList) xo.getChild(TaxonList.class);
    if (taxa == null)
        taxa = (Tree) xo.getChild(Tree.class);
    Alignment alignment = (Alignment) xo.getChild(Alignment.class);
    LinkageConstraints lc = (LinkageConstraints) xo.getChild(LinkageConstraints.class);
    boolean fixedReferenceTree = false;
    if (xo.hasAttribute("fixedReferenceTree")) {
        fixedReferenceTree = xo.getBooleanAttribute("fixedReferenceTree");
    }
    MetagenomeData md = new MetagenomeData(taxa, alignment, lc, fixedReferenceTree);
    return md;
}

Example 14 with Alignment

use of dr.evolution.alignment.Alignment in project beast-mcmc by beast-dev.

the class TKF91LikelihoodParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    TreeModel tree = (TreeModel) xo.getChild(TreeModel.class);
    Alignment alignment = (Alignment) xo.getChild(Alignment.class);
    GammaSiteModel siteModel = (GammaSiteModel) xo.getChild(GammaSiteModel.class);
    TKF91Model tkfModel = (TKF91Model) xo.getChild(TKF91Model.class);
    return new TKF91Likelihood(tree, alignment, siteModel, tkfModel);
}

Example 15 with Alignment

use of dr.evolution.alignment.Alignment in project beast-mcmc by beast-dev.

the class LineageSitePatternsParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Alignment alignment = (Alignment) xo.getChild(Alignment.class);
    TaxonList taxa = null;
    int from = 0;
    int to = -1;
    int every = xo.getAttribute(EVERY, 1);
    boolean strip = xo.getAttribute(STRIP, true);
    boolean unique = xo.getAttribute(UNIQUE, true);
    if (xo.hasAttribute(FROM)) {
        from = xo.getIntegerAttribute(FROM) - 1;
        if (from < 0)
            throw new XMLParseException("illegal 'from' attribute in patterns element");
    }
    if (xo.hasAttribute(TO)) {
        to = xo.getIntegerAttribute(TO) - 1;
        if (to < 0 || to < from)
            throw new XMLParseException("illegal 'to' attribute in patterns element");
    }
    if (every <= 0)
        throw new XMLParseException("illegal 'every' attribute in patterns element");
    if (xo.hasChildNamed(TAXON_LIST)) {
        taxa = (TaxonList) xo.getElementFirstChild(TAXON_LIST);
    }
    if (from > alignment.getSiteCount())
        throw new XMLParseException("illegal 'from' attribute in patterns element");
    if (to > alignment.getSiteCount())
        throw new XMLParseException("illegal 'to' attribute in patterns element");
    LineageSitePatterns patterns = new LineageSitePatterns(alignment, taxa, from, to, every, strip, unique);
    int f = from + 1;
    // fixed a *display* error by adding + 1 for consistency with f = from + 1
    int t = to + 1;
    if (to == -1)
        t = alignment.getSiteCount();
    if (xo.hasAttribute(XMLParser.ID)) {
        final Logger logger = Logger.getLogger("dr.evoxml");
        logger.info("Site patterns '" + xo.getId() + "' created from positions " + Integer.toString(f) + "-" + Integer.toString(t) + " of alignment '" + alignment.getId() + "'");
        if (every > 1) {
            logger.info("  only using every " + every + " site");
        }
        logger.info("  pattern count = " + patterns.getPatternCount());
    }
    return patterns;
}