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

Example 6 with FlexibleTree

use of dr.evolution.tree.FlexibleTree 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 7 with FlexibleTree

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

the class TaxaOriginTrait method tabulateOrigins.

private void tabulateOrigins() {
    HashMap<String, Integer> countsMap = new HashMap<String, Integer>();
    int count = 0;
    for (FlexibleTree currentTree : trees) {
        if (count % 1 == 0) {
            System.out.println("Doing tree " + count);
        }
        HashMap<String, String> results = getIncomingJumpOrigins(currentTree);
        for (String key : results.keySet()) {
            int oldCount = countsMap.containsKey(results.get(key)) ? countsMap.get(results.get(key)) : 0;
            countsMap.put(results.get(key), oldCount + 1);
        }
        count++;
    }
    try {
        BufferedWriter outWriter = new BufferedWriter(new FileWriter(fileNameRoot + ".csv"));
        for (String key : countsMap.keySet()) {
            outWriter.write(key + "," + countsMap.get(key) + "\n");
        }
        outWriter.flush();
    } catch (IOException e) {
        System.out.println("Failed to write to file");
    }
}

Example 8 with FlexibleTree

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

the class TaxaOriginTrait method getTraitName.

private String getTraitName() {
    FlexibleTree tree = trees[0];
    String traitName = null;
    for (int i = 0; i < tree.getExternalNodeCount(); i++) {
        NodeRef node = tree.getExternalNode(i);
        for (String taxaName : taxaNames) {
            if (tree.getNodeTaxon(node).getId().equals(taxaName)) {
                String attributeValue = (String) tree.getNodeAttribute(node, attributeName);
                if (traitName != null && !traitName.equals(attributeValue)) {
                    throw new RuntimeException("Not all taxa given have the same trait value");
                } else {
                    traitName = attributeValue;
                }
            }
        }
    }
    return traitName;
}

Example 9 with FlexibleTree

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

the class SimulateTrait method simulate.

/**
	 * simulates a trait ona tree.
	 * @param clone if true, use copy of the tree, otherwise use given tree
	 * @return the simulated tree.
	 */
public Tree simulate(Tree tree, double value, boolean clone) {
    Tree binaryTree = null;
    if (clone) {
        binaryTree = new FlexibleTree(tree);
        ((FlexibleTree) binaryTree).resolveTree();
    } else {
        binaryTree = tree;
    }
    simulate((MutableTree) binaryTree, binaryTree.getRoot(), value);
    return binaryTree;
}

Example 10 with FlexibleTree

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

the class NewickImporter 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;
}