Examples with Loggable dr.inference.loggers.Loggable used on opensource projects

Example 1 with Loggable

use of dr.inference.loggers.Loggable in project beast-mcmc by beast-dev.

the class TreeLoggerParser method parseXMLParameters.

protected void parseXMLParameters(XMLObject xo) throws XMLParseException {
    // reset this every time...
    branchRates = null;
    tree = (Tree) xo.getChild(Tree.class);
    title = xo.getAttribute(TITLE, "");
    nexusFormat = xo.getAttribute(NEXUS_FORMAT, false);
    sortTranslationTable = xo.getAttribute(SORT_TRANSLATION_TABLE, true);
    boolean substitutions = xo.getAttribute(BRANCH_LENGTHS, "").equals(SUBSTITUTIONS);
    List<TreeAttributeProvider> taps = new ArrayList<TreeAttributeProvider>();
    List<TreeTraitProvider> ttps = new ArrayList<TreeTraitProvider>();
    // ttps2 are for TTPs that are not specified within a Trait element. These are only
    // included if not already added through a trait element to avoid duplication of
    // (in particular) the BranchRates which is required for substitution trees.
    List<TreeTraitProvider> ttps2 = new ArrayList<TreeTraitProvider>();
    for (int i = 0; i < xo.getChildCount(); i++) {
        Object cxo = xo.getChild(i);
        if (cxo instanceof Likelihood) {
            final Likelihood likelihood = (Likelihood) cxo;
            taps.add(new TreeAttributeProvider() {

                public String[] getTreeAttributeLabel() {
                    return new String[] { "lnP" };
                }

                public String[] getAttributeForTree(Tree tree) {
                    return new String[] { Double.toString(likelihood.getLogLikelihood()) };
                }
            });
        }
        if (cxo instanceof TreeAttributeProvider) {
            taps.add((TreeAttributeProvider) cxo);
        }
        if (cxo instanceof TreeTraitProvider) {
            if (xo.hasAttribute(FILTER_TRAITS)) {
                String[] matches = ((String) xo.getAttribute(FILTER_TRAITS)).split("[\\s,]+");
                TreeTraitProvider ttp = (TreeTraitProvider) cxo;
                TreeTrait[] traits = ttp.getTreeTraits();
                List<TreeTrait> filteredTraits = new ArrayList<TreeTrait>();
                for (String match : matches) {
                    for (TreeTrait trait : traits) {
                        if (trait.getTraitName().startsWith(match)) {
                            filteredTraits.add(trait);
                        }
                    }
                }
                if (filteredTraits.size() > 0) {
                    ttps2.add(new TreeTraitProvider.Helper(filteredTraits));
                }
            } else {
                // Add all of them
                ttps2.add((TreeTraitProvider) cxo);
            }
        }
        if (cxo instanceof XMLObject) {
            XMLObject xco = (XMLObject) cxo;
            if (xco.getName().equals(TREE_TRAIT)) {
                TreeTraitProvider ttp = (TreeTraitProvider) xco.getChild(TreeTraitProvider.class);
                if (xco.hasAttribute(NAME)) {
                    // a specific named trait is required (optionally with a tag to name it in the tree file)
                    String name = xco.getStringAttribute(NAME);
                    final TreeTrait trait = ttp.getTreeTrait(name);
                    if (trait == null) {
                        String childName = "TreeTraitProvider";
                        if (ttp instanceof Likelihood) {
                            childName = ((Likelihood) ttp).prettyName();
                        } else if (ttp instanceof Model) {
                            childName = ((Model) ttp).getModelName();
                        }
                        throw new XMLParseException("Trait named, " + name + ", not found for " + childName);
                    }
                    final String tag;
                    if (xco.hasAttribute(TAG)) {
                        tag = xco.getStringAttribute(TAG);
                    } else {
                        tag = name;
                    }
                    ttps.add(new TreeTraitProvider.Helper(tag, new TreeTrait() {

                        public String getTraitName() {
                            return tag;
                        }

                        public Intent getIntent() {
                            return trait.getIntent();
                        }

                        public Class getTraitClass() {
                            return trait.getTraitClass();
                        }

                        public Object getTrait(Tree tree, NodeRef node) {
                            return trait.getTrait(tree, node);
                        }

                        public String getTraitString(Tree tree, NodeRef node) {
                            return trait.getTraitString(tree, node);
                        }

                        public boolean getLoggable() {
                            return trait.getLoggable();
                        }
                    }));
                } else if (xo.hasAttribute(FILTER_TRAITS)) {
                    // else a filter attribute is given to ask for all traits that starts with a specific
                    // string
                    String[] matches = ((String) xo.getAttribute(FILTER_TRAITS)).split("[\\s,]+");
                    TreeTrait[] traits = ttp.getTreeTraits();
                    List<TreeTrait> filteredTraits = new ArrayList<TreeTrait>();
                    for (String match : matches) {
                        for (TreeTrait trait : traits) {
                            if (trait.getTraitName().startsWith(match)) {
                                filteredTraits.add(trait);
                            }
                        }
                    }
                    if (filteredTraits.size() > 0) {
                        ttps.add(new TreeTraitProvider.Helper(filteredTraits));
                    }
                } else {
                    // neither named or filtered traits so just add them all
                    ttps.add(ttp);
                }
            }
        }
        // be able to put arbitrary statistics in as tree attributes
        if (cxo instanceof Loggable) {
            final Loggable loggable = (Loggable) cxo;
            taps.add(new TreeAttributeProvider() {

                public String[] getTreeAttributeLabel() {
                    String[] labels = new String[loggable.getColumns().length];
                    for (int i = 0; i < loggable.getColumns().length; i++) {
                        labels[i] = loggable.getColumns()[i].getLabel();
                    }
                    return labels;
                }

                public String[] getAttributeForTree(Tree tree) {
                    String[] values = new String[loggable.getColumns().length];
                    for (int i = 0; i < loggable.getColumns().length; i++) {
                        values[i] = loggable.getColumns()[i].getFormatted();
                    }
                    return values;
                }
            });
        }
    }
    // inclusion of the codon partitioned robust counting TTP...
    if (ttps2.size() > 0) {
        ttps.addAll(ttps2);
    }
    if (substitutions) {
        branchRates = (BranchRates) xo.getChild(BranchRates.class);
    }
    if (substitutions && branchRates == null) {
        throw new XMLParseException("To log trees in units of substitutions a BranchRateModel must be provided");
    }
    // logEvery of zero only displays at the end
    logEvery = xo.getAttribute(LOG_EVERY, 0);
    //        double normaliseMeanRateTo = xo.getAttribute(NORMALISE_MEAN_RATE_TO, Double.NaN);
    // decimal places
    final int dp = xo.getAttribute(DECIMAL_PLACES, -1);
    if (dp != -1) {
        format = NumberFormat.getNumberInstance(Locale.ENGLISH);
        format.setMaximumFractionDigits(dp);
    }
    final PrintWriter pw = getLogFile(xo, getParserName());
    formatter = new TabDelimitedFormatter(pw);
    treeAttributeProviders = new TreeAttributeProvider[taps.size()];
    taps.toArray(treeAttributeProviders);
    treeTraitProviders = new TreeTraitProvider[ttps.size()];
    ttps.toArray(treeTraitProviders);
    // I think the default should be to have names rather than numbers, thus the false default - AJD
    // I think the default should be numbers - using names results in larger files and end user never
    // sees the numbers anyway as any software loading the nexus files does the translation - JH
    mapNames = xo.getAttribute(MAP_NAMES, true);
    condition = logEvery == 0 ? (TreeLogger.LogUpon) xo.getChild(TreeLogger.LogUpon.class) : null;
}