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

Example 16 with NexusImporter

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

the class TreeLengthFinder method report.

/**
     * Recursively analyzes trees files.
     *
     * @param name       the file to analyze (if this is a directory then the files within it are analyzed)
     * @param burnin     the burnin to use
     */
private void report(String name, int burnin) {
    double treeLength = 0.0;
    int count = 0;
    try {
        FileReader fileReader = new FileReader(new File(name));
        TreeImporter importer = new NexusImporter(fileReader);
        while (importer.hasTree()) {
            Tree tree = importer.importNextTree();
            if (count >= burnin) {
                treeLength += TreeLength.FACTORY.createStatistic().getSummaryStatistic(tree)[0];
            }
            count++;
        }
        treeLength /= (count - burnin);
        System.out.println(name + "\t" + burnin + "\t" + treeLength);
    } catch (Importer.ImportException e) {
        System.err.println("Error Parsing Input Tree: " + e.getMessage());
    } catch (IOException e) {
        System.err.println("Error Parsing Input Tree: " + e.getMessage());
    }
}

Example 17 with NexusImporter

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

the class TaxaOriginTrait method main.

/*
    * Arguments:
    * 0: Trait name
    * 1: File name for list of taxaNames of interest
    * 2: File name for trees (output from BranchJumpPlotter)
    * 3: Output file name root
    * */
public static void main(String[] args) {
    try {
        BufferedReader taxonReader = new BufferedReader(new FileReader(args[1]));
        HashSet<String> tempTaxa = new HashSet<String>();
        String line;
        while ((line = taxonReader.readLine()) != null) {
            tempTaxa.add(line);
        }
        String[] taxa = tempTaxa.toArray(new String[tempTaxa.size()]);
        NexusImporter importer = new NexusImporter(new FileReader(args[2]));
        importer.setSuppressWarnings(true);
        ArrayList<FlexibleTree> tempTrees = new ArrayList<FlexibleTree>();
        int count = 0;
        while (importer.hasTree()) {
            if (count % 100 == 0) {
                System.out.println("Loaded " + count + " trees");
            }
            tempTrees.add((FlexibleTree) importer.importNextTree());
            count++;
        }
        FlexibleTree[] trees = tempTrees.toArray(new FlexibleTree[tempTrees.size()]);
        TaxaOriginTrait examiner = new TaxaOriginTrait(taxa, trees, args[0], args[3]);
        examiner.tabulateOrigins();
    } catch (IOException e) {
        System.out.println("Failed to read files");
    } catch (Importer.ImportException e) {
        System.out.println("Failed to import trees");
    }
}

Example 18 with NexusImporter

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

the class OrderNexusTranslationTable method main.

public static void main(String[] args) throws Importer.ImportException, IOException {
    NexusImporter importer = new NexusImporter(new FileReader(args[0]));
    Tree[] trees = importer.importTrees(null);
    System.out.println("Read " + trees.length + " trees from " + args[0]);
    String newFileName = args[0] + ".new";
    PrintStream ps = new PrintStream(new FileOutputStream(newFileName));
    NexusExporter exporter = new NexusExporter(ps);
    exporter.setTreePrefix("STATE_");
    NumberFormat format = NumberFormat.getNumberInstance();
    format.setMaximumFractionDigits(7);
    exporter.setNumberFormat(format);
    exporter.setSortedTranslationTable(true);
    exporter.exportTrees(trees, false);
    ps.flush();
    ps.close();
    System.out.println("Wrote " + trees.length + " trees to " + newFileName);
}

Example 19 with NexusImporter

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

the class CoalGenFrame method importFromFile.

protected void importFromFile(File file) throws IOException, Importer.ImportException {
    BufferedReader reader = new BufferedReader(new FileReader(file));
    String line = reader.readLine();
    Tree tree;
    if (line.toUpperCase().startsWith("#NEXUS")) {
        NexusImporter importer = new NexusImporter(reader);
        tree = importer.importTree(null);
    } else {
        NewickImporter importer = new NewickImporter(reader);
        tree = importer.importTree(null);
    }
    data.taxonList = tree;
    statusLabel.setText(Integer.toString(data.taxonList.getTaxonCount()) + " taxa loaded.");
    reader.close();
    fireTaxaChanged();
}

Example 20 with NexusImporter

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

the class GetNSCountsFromTrees method analyze.

private void analyze(File inputFile, int burnin, BranchSet branchSet, List<Set> inclusionSets, List<Set> exclusionSets, double[] siteList) {
    if (summary) {
        resultsStream.print("tree" + SEP + "cN" + SEP + "uN" + SEP + "cS" + SEP + "uS" + SEP + "cNrate" + SEP + "cSrate" + SEP + "dN/dS" + "\n");
    } else {
        resultsStream.print("tree" + SEP + "branch" + SEP + "N/S" + SEP + "site" + SEP + "height/date" + SEP + "fromState" + SEP + "toState");
        if (branchInfo) {
            resultsStream.print(SEP + "branchLength" + SEP + "branchCN/S" + SEP + "branchUN/S" + "\n");
        } else {
            resultsStream.print("\n");
        }
    }
    int totalTrees = 10000;
    int totalStars = 0;
    System.out.println("Reading and analyzing trees (bar assumes 10,000 trees)...");
    System.out.println("0              25             50             75            100");
    System.out.println("|--------------|--------------|--------------|--------------|");
    int stepSize = totalTrees / 60;
    if (stepSize < 1)
        stepSize = 1;
    int count = 0;
    int treeUsed = 1;
    try {
        FileReader fileReader = new FileReader(inputFile);
        TreeImporter importer = new NexusImporter(fileReader);
        while (importer.hasTree()) {
            Tree tree = importer.importNextTree();
            if (count >= burnin) {
                getNSCounts(tree, treeUsed, branchSet, inclusionSets, exclusionSets, siteList);
                treeUsed++;
            }
            count++;
            if (totalTrees > 0 && totalTrees % stepSize == 0) {
                System.out.print("*");
                totalStars++;
                if (totalStars % 61 == 0)
                    System.out.print("\n");
                System.out.flush();
            }
            totalTrees++;
        }
        System.out.print("\n");
    } catch (Importer.ImportException e) {
        progressStream.println("Error Parsing Input Tree: " + e.getMessage());
    } catch (IOException e) {
        progressStream.println("Error Parsing Input Tree: " + e.getMessage());
    }
}