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

Example 26 with Tree

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

the class RateStatisticParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    final String name = xo.getAttribute(Statistic.NAME, xo.getId());
    final Tree tree = (Tree) xo.getChild(Tree.class);
    final BranchRateModel branchRateModel = (BranchRateModel) xo.getChild(BranchRateModel.class);
    final boolean internal = xo.getBooleanAttribute("internal");
    final boolean external = xo.getBooleanAttribute("external");
    if (!(internal || external)) {
        throw new XMLParseException("At least one of internal and external must be true!");
    }
    final String mode = xo.getStringAttribute(MODE);
    return new RateStatistic(name, tree, branchRateModel, external, internal, mode);
}

Example 27 with Tree

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

the class SpeciesTreeStatisticParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    String name = xo.getAttribute(Statistic.NAME, xo.getId());
    Tree speciesTree = (Tree) xo.getElementFirstChild("speciesTree");
    Tree popTree = (Tree) xo.getElementFirstChild("populationTree");
    return new SpeciesTreeStatistic(name, speciesTree, popTree);
}

Example 28 with Tree

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

the class TerminalBranchStatisticParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    String name = xo.getAttribute(Statistic.NAME, xo.getId());
    Tree tree = (Tree) xo.getChild(Tree.class);
    return new TerminalBranchStatistic(name, tree);
}

Example 29 with Tree

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

the class TimeSlicer method readAndAnalyzeTrees.

//    private List<Tree> importTrees(String treeFileName, int burnin) throws IOException, Importer.ImportException {
//
//        int totalTrees = 10000;
//
//        progressStream.println("Reading trees (bar assumes 10,000 trees)...");
//        progressStream.println("0              25             50             75            100");
//        progressStream.println("|--------------|--------------|--------------|--------------|");
//
//        int stepSize = totalTrees / 60;
//        if (stepSize < 1) stepSize = 1;
//
//        List<Tree> treeList = new ArrayList<Tree>();
//        BufferedReader reader1 = new BufferedReader(new FileReader(treeFileName));
//
//        String line1 = reader1.readLine();
//        TreeImporter importer1;
//        if (line1.toUpperCase().startsWith("#NEXUS")) {
//            importer1 = new NexusImporter(new FileReader(treeFileName));
//        } else {
//            importer1 = new NewickImporter(new FileReader(treeFileName));
//        }
//        totalTrees = 0;
//        while (importer1.hasTree()) {
//            Tree treeTime = importer1.importNextTree();
//
//            if (totalTrees > burnin)
//                treeList.add(treeTime);
//
//            if (totalTrees > 0 && totalTrees % stepSize == 0) {
//                progressStream.print("*");
//                progressStream.flush();
//            }
//            totalTrees++;
//        }
//        return treeList;
//    }
private void readAndAnalyzeTrees(String treeFileName, int burnin, int skipEvery, String[] traits, double[] slices, boolean impute, boolean trueNoise, Normalization normalize, boolean divideByBranchLength, BranchSet branchset, Set taxaSet) throws IOException, Importer.ImportException {
    int totalTrees = 10000;
    int totalStars = 0;
    progressStream.println("Reading and analyzing trees (bar assumes 10,000 trees)...");
    progressStream.println("0              25             50             75            100");
    progressStream.println("|--------------|--------------|--------------|--------------|");
    int stepSize = totalTrees / 60;
    if (stepSize < 1)
        stepSize = 1;
    BufferedReader reader1 = new BufferedReader(new FileReader(treeFileName));
    String line1 = reader1.readLine();
    TreeImporter importer1;
    if (line1.toUpperCase().startsWith("#NEXUS")) {
        importer1 = new NexusImporter(new FileReader(treeFileName));
    } else {
        importer1 = new NewickImporter(new FileReader(treeFileName));
    }
    totalTrees = 0;
    while (importer1.hasTree()) {
        Tree treeTime = importer1.importNextTree();
        if (totalTrees % skipEvery == 0) {
            treesRead++;
            if (totalTrees >= burnin) {
                analyzeTree(treeTime, traits, slices, impute, trueNoise, normalize, divideByBranchLength, branchset, taxaSet);
            }
        }
        if (totalTrees > 0 && totalTrees % stepSize == 0) {
            progressStream.print("*");
            totalStars++;
            if (totalStars % 61 == 0)
                progressStream.print("\n");
            progressStream.flush();
        }
        totalTrees++;
    }
    progressStream.print("\n");
}

Example 30 with Tree

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

the class GetDateFromTree method getRandomTree.

private static Tree getRandomTree() {
    Random random = new Random();
    // [1, 10]
    int c = random.nextInt(10) + 1;
    // [1000, 10000]
    int tId = random.nextInt(9000) + 1000;
    try {
        System.out.println("randomly get " + tId + "th tree from " + pathInput + c + inputFileName + "\n\n");
        FileReader fileReader = new FileReader(pathInput + c + inputFileName);
        // many trees
        GetDateFromTree getDateFromTree = new GetDateFromTree(fileReader);
        int totalTrees = 0;
        try {
            while (getDateFromTree.hasTree()) {
                Tree tree = getDateFromTree.importNextTree();
                totalTrees++;
                if (totalTrees == tId) {
                    return tree;
                }
            }
        } catch (ImportException e) {
            System.err.println("Error Parsing Input Tree: " + e.getMessage());
            return null;
        }
        fileReader.close();
    } catch (FileNotFoundException e) {
        //To change body of catch statement use File | Settings | File Templates.
        e.printStackTrace();
    } catch (IOException e) {
        //To change body of catch statement use File | Settings | File Templates.
        e.printStackTrace();
    }
    return null;
}