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

Example 31 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 32 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 33 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 34 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;
}

Example 35 with Tree

use of dr.evolution.tree.Tree 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");
}