Examples with NewickImporter dr.evolution.io.NewickImporter used on opensource projects

Example 6 with NewickImporter

use of dr.evolution.io.NewickImporter in project beast-mcmc by beast-dev.

the class TreeSpaceLogger method readTrees.

private void readTrees(String filename) {
    try {
        FileReader fr = new FileReader(new File(filename));
        BufferedReader br = new BufferedReader(fr);
        String line;
        List<Tree> trees = new ArrayList<Tree>();
        List<Integer> islands = new ArrayList<Integer>();
        while ((line = br.readLine()) != null) {
            // read trees
            String[] tokens = line.split("\\s++");
            NewickImporter importer = new NewickImporter(line);
            Tree t = importer.importNextTree();
            trees.add(t);
            islands.add(Integer.parseInt(tokens[0]));
        }
        br.close();
        fr.close();
        this.trees = new String[trees.size()];
        this.islands = new int[trees.size()];
        int maxIsland = 0;
        for (int i = 0; i < trees.size(); i++) {
            Tree tree = trees.get(i);
            String newick = TreeUtils.uniqueNewick(tree, tree.getRoot());
            this.trees[i] = newick;
            this.islands[i] = islands.get(i) - 1;
            if (islands.get(i) > maxIsland) {
                maxIsland = islands.get(i);
            }
        }
        transitions = new int[trees.size()][trees.size()];
        steps = new int[trees.size()][trees.size()];
        islandTransitions = new int[maxIsland][maxIsland];
        islandDwellTimes = new int[maxIsland];
    //			pathes = new HashMap[trees.size()][trees.size()];
    //			for (int i = 0; i < trees.size(); i++) {
    //				for (int j = 0; j < trees.size(); j++) {
    //					pathes[i][j] = new HashMap<String, Integer>();
    //				}
    //			}
    } catch (FileNotFoundException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    } catch (IOException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    } catch (ImportException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
}

Example 7 with NewickImporter

use of dr.evolution.io.NewickImporter in project beast-mcmc by beast-dev.

the class ExchangeOperatorTest method testWideExchangeOperator2.

public void testWideExchangeOperator2() throws IOException, ImportException {
    // probability of picking (A,B) node is 1/(2n-2) = 1/8
    // probability of swapping with D is 1/2
    // total = 1/16
    //probability of picking {D} node is 1/(2n-2) = 1/8
    //probability of picking {A,B} is 1/5
    // total = 1/40
    //total = 1/16 + 1/40 = 0.0625 + 0.025 = 0.0875
    // new test:
    // probability of picking (A,B) node is 1/(2n-2) = 1/8
    // probability of swapping with D is 1/(2n-3) = 1/7
    // total = 1/56
    //probability of picking {D} node is 1/(2n-2) = 1/8
    //probability of picking {A,B} is 1/(2n-3) = 1/7
    // total = 1/56
    //total = 1/56 + 1/56 = 1/28
    System.out.println("Test 1: Forward");
    String treeMatch = "(((D,C),(A,B)),E);";
    int count = 0;
    int reps = 1000000;
    for (int i = 0; i < reps; i++) {
        TreeModel treeModel = new TreeModel("treeModel", tree5);
        ExchangeOperator operator = new ExchangeOperator(ExchangeOperator.WIDE, treeModel, 1.0);
        operator.doOperation();
        String tree = TreeUtils.newickNoLengths(treeModel);
        if (tree.equals(treeMatch)) {
            count += 1;
        }
    }
    double p_1 = (double) count / (double) reps;
    System.out.println("Number of proposals:\t" + count);
    System.out.println("Number of tries:\t" + reps);
    System.out.println("Number of ratio:\t" + p_1);
    System.out.println("Number of expected ratio:\t" + 1.0 / 28.0);
    assertExpectation(1.0 / 28.0, p_1, reps);
    // since this operator is supposed to be symmetric it got a hastings ratio of one
    // this means, it should propose the same move just backwards with the same probability
    // BUT:
    // (((D:2.0,C:2.0):1.0,(A:1.0,B:1.0):2.0):1.0,E:4.0) -> ((((A,B),C),D),E)
    // probability of picking (A,B) node is 1/(2n-2) = 1/8
    // probability of swapping with D is 1/3
    // total = 1/24
    //probability of picking {D} node is 1/(2n-2) = 1/8
    //probability of picking {A,B} is 1/4
    // total = 1/32
    //total = 1/24 + 1/32 = 7/96 = 0.07291666666
    // new test:
    // probability of picking (A,B) node is 1/(2n-2) = 1/8
    // probability of swapping with D is 1/(2n-3) = 1/7
    // total = 1/56
    //probability of picking {D} node is 1/(2n-2) = 1/8
    //probability of picking {A,B} is 1/(2n-3) = 1/7
    // total = 1/56
    //total = 1/56 + 1/56 = 1/28
    System.out.println("Test 2: Backward");
    treeMatch = "((((A,B),C),D),E);";
    NewickImporter importer = new NewickImporter("(((D:2.0,C:2.0):1.0,(A:1.0,B:1.0):2.0):1.0,E:4.0);");
    FlexibleTree tree5_2 = (FlexibleTree) importer.importTree(null);
    count = 0;
    for (int i = 0; i < reps; i++) {
        TreeModel treeModel = new TreeModel("treeModel", tree5_2);
        ExchangeOperator operator = new ExchangeOperator(ExchangeOperator.WIDE, treeModel, 1.0);
        operator.doOperation();
        String tree = TreeUtils.newickNoLengths(treeModel);
        if (tree.equals(treeMatch)) {
            count += 1;
        }
    }
    double p_2 = (double) count / (double) reps;
    System.out.println("Number of proposals:\t" + count);
    System.out.println("Number of tries:\t" + reps);
    System.out.println("Number of ratio:\t" + p_2);
    System.out.println("Number of expected ratio:\t" + 1.0 / 28.0);
    assertExpectation(1.0 / 28.0, p_2, reps);
}

Example 8 with NewickImporter

use of dr.evolution.io.NewickImporter in project beast-mcmc by beast-dev.

the class RLYModelTest method setUp.

public void setUp() throws Exception {
    super.setUp();
    MathUtils.setSeed(666);
    NewickImporter importer = new NewickImporter("(((((A:1.0,B:1.0):1.0,C:2.0),D:3.0):1.0, E:4.0),F:5.0);");
    tree = (FlexibleTree) importer.importTree(null);
}

Example 9 with NewickImporter

use of dr.evolution.io.NewickImporter in project beast-mcmc by beast-dev.

the class YuleLikelihoodTest method setUp.

public void setUp() throws Exception {
    super.setUp();
    NewickImporter importer = new NewickImporter("((1:1.0,2:1.0):1.0,(3:1.0,4:1.0):1.0);");
    tree = (FlexibleTree) importer.importTree(null);
}

Example 10 with NewickImporter

use of dr.evolution.io.NewickImporter in project beast-mcmc by beast-dev.

the class YuleModelTest method setUp.

public void setUp() throws Exception {
    super.setUp();
    MathUtils.setSeed(666);
    NewickImporter importer = new NewickImporter("((1:1.0,2:1.0):1.0,(3:1.0,4:1.0):1.0);");
    tree = (FlexibleTree) importer.importTree(null);
}