Examples with FlexibleNode dr.evolution.tree.FlexibleNode used on opensource projects

Example 1 with FlexibleNode

use of dr.evolution.tree.FlexibleNode in project beast-mcmc by beast-dev.

the class TiterImporter method readExternalNode.

/**
     * Reads an external node in.
     */
private FlexibleNode readExternalNode(TaxonList taxonList) throws IOException, ImportException {
    FlexibleNode node = new FlexibleNode();
    String label = readToken(":(),;");
    Taxon taxon;
    if (taxonList != null) {
        // if a taxon list is given then the taxon must be in it...
        int index = taxonList.getTaxonIndex(label);
        if (index != -1) {
            taxon = taxonList.getTaxon(index);
        } else {
            throw new UnknownTaxonException("Taxon in tree, '" + label + "' is unknown");
        }
    } else {
        // No taxon list given so create new taxa
        taxon = new Taxon(label);
    }
    node.setTaxon(taxon);
    return node;
}

Example 2 with FlexibleNode

use of dr.evolution.tree.FlexibleNode in project beast-mcmc by beast-dev.

the class TiterImporter method readInternalNode.

/**
     * Reads a node in. This could be a polytomy. Calls readBranch on each branch
     * in the node.
     */
private FlexibleNode readInternalNode(TaxonList taxonList) throws IOException, ImportException {
    FlexibleNode node = new FlexibleNode();
    // read the opening '('
    final char ch = readCharacter();
    assert ch == '(';
    // read the first child
    node.addChild(readBranch(taxonList));
    // an internal node must have at least 2 children
    if (getLastDelimiter() != ',') {
        throw new BadFormatException("Expecting ',' in tree, but got '" + (char) getLastDelimiter() + "'");
    }
    // read subsequent children
    do {
        node.addChild(readBranch(taxonList));
    } while (getLastDelimiter() == ',');
    // should have had a closing ')'
    if (getLastDelimiter() != ')') {
        throw new BadFormatException("Missing closing ')' in tree");
    }
    // If there is a label before the colon, store it:
    try {
        String label = readToken(",():;");
        if (label.length() > 0) {
            node.setAttribute("label", label);
        }
    } catch (IOException ioe) {
    // probably an end of file without a terminal ';'
    // we are going to allow this and return the nodes...
    }
    return node;
}

Example 3 with FlexibleNode

use of dr.evolution.tree.FlexibleNode in project beast-mcmc by beast-dev.

the class TiterImporter method importTrees.

/**
     * importTrees.
     */
public Tree[] importTrees(TaxonList taxonList) throws IOException, ImportException {
    boolean done = false;
    ArrayList<FlexibleTree> array = new ArrayList<FlexibleTree>();
    do {
        try {
            skipUntil("(");
            unreadCharacter('(');
            FlexibleNode root = readInternalNode(taxonList);
            FlexibleTree tree = new FlexibleTree(root, false, true);
            array.add(tree);
            if (taxonList == null) {
                taxonList = tree;
            }
            if (readCharacter() != ';') {
                throw new BadFormatException("Expecting ';' after tree");
            }
        } catch (EOFException e) {
            done = true;
        }
    } while (!done);
    Tree[] trees = new Tree[array.size()];
    array.toArray(trees);
    return trees;
}

Example 4 with FlexibleNode

use of dr.evolution.tree.FlexibleNode in project beast-mcmc by beast-dev.

the class TiterImporter method readBranch.

/**
     * Reads a branch in. This could be a node or a tip (calls readNode or readTip
     * accordingly). It then reads the branch length and SimpleNode that will
     * point at the new node or tip.
     */
private FlexibleNode readBranch(TaxonList taxonList) throws IOException, ImportException {
    double length = 0.0;
    FlexibleNode branch;
    if (nextCharacter() == '(') {
        // is an internal node
        branch = readInternalNode(taxonList);
    } else {
        // is an external node
        branch = readExternalNode(taxonList);
    }
    final String comment = getLastMetaComment();
    if (comment != null) {
        branch.setAttribute(COMMENT, comment);
        clearLastMetaComment();
    }
    if (getLastDelimiter() == ':') {
        length = readDouble(",():;");
    }
    branch.setLength(length);
    return branch;
}

Example 5 with FlexibleNode

use of dr.evolution.tree.FlexibleNode in project beast-mcmc by beast-dev.

the class GetDateFromTree method getDate.

private static void getDate(String curD, int index, Tree treeOne) throws ImportException {
    // many trees
    double rootHeight;
    DecimalFormat twoDForm = new DecimalFormat("####0.##");
    Tree[] trees = new Tree[combiTrees];
    double[][] tips = new double[combiTrees][treeOne.getExternalNodeCount() + 1];
    double[] origins = new double[trees.length];
    trees[0] = treeOne;
    for (int t = 1; t < combiTrees; t++) {
        trees[t] = getRandomTree();
        if (trees[t] == null)
            throw new ImportException("get null random tree");
    // System.out.println(t + " => " + trees[t].toString());
    }
    for (int t = 0; t < trees.length; t++) {
        System.out.println(t + " => " + trees[t]);
        for (int i = 0; i < trees[t].getTaxonCount(); i++) {
            FlexibleNode node = (FlexibleNode) trees[t].getExternalNode(i);
            // System.out.println(node.getTaxon() + " has " + node.getHeight());
            tips[t][Integer.parseInt(node.getTaxon().getId())] = node.getHeight();
        }
        rootHeight = ((FlexibleNode) trees[t].getRoot()).getHeight();
        origins[t] = Double.valueOf(twoDForm.format(rootHeight + 100.0));
        System.out.println("tree " + t + " root height = " + rootHeight + " origin = " + origins[t]);
        System.out.println("\n");
    }
    if (index < 0) {
        printXML(tips[0]);
    } else {
        try {
            outputBDSSXML(curD, index, tips, origins, trees);
        // outputExponetialXML(curD, index, tips, origins, trees);
        } catch (IOException e) {
            // To change body of catch statement use File | Settings | File Templates.
            e.printStackTrace();
        }
    }
    System.out.println("\n");
}