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

Example 16 with Importer

use of dr.evolution.io.Importer 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());
    }
}

Example 17 with Importer

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

the class GetAncestralSequenceFromSplitTrait method analyze.

/**
     * Recursively analyzes log files.
     *
     * @param treeAnnotatorInputFile       the file to analyze (if this is a directory then the files within it are analyzed)
     * @throws dr.inference.trace.TraceException
     *          if the trace file is in the wrong format or corrupted
     */
private void analyze(File treeAnnotatorInputFile) throws TraceException {
    try {
        FileReader fileReader = new FileReader(treeAnnotatorInputFile);
        TreeImporter importer = new NexusImporter(fileReader);
        FlexibleTree tree = (FlexibleTree) importer.importNextTree();
        for (int i = 0; i < tree.getNodeCount(); i++) {
            Hashtable<Integer, State> states = new Hashtable<Integer, State>();
            for (Iterator<String> j = tree.getNodeAttributeNames(tree.getNode(i)); j.hasNext(); ) {
                String name = j.next();
                if (name.indexOf("states_") >= 0) {
                    Integer d = Integer.parseInt(name.replaceFirst("states_", "").replaceFirst("\\..+", ""));
                    //= new State(name.);
                    State s;
                    if (states.containsKey(d)) {
                        s = states.get(d);
                    } else {
                        s = new State(d);
                    }
                    if (name.matches("states_" + d + ".prob")) {
                        Object o = tree.getNodeAttribute(tree.getNode(i), name);
                        double probability = (Double) o;
                        s.setProbability(probability);
                    } else if (name.matches("states_" + d)) {
                        Object o = tree.getNodeAttribute(tree.getNode(i), name);
                        String value = (String) o;
                        s.setState(value.replaceAll("\"", ""));
                    } else if (name.matches("states_" + d + ".set.prob")) {
                        /* Not necessary but lets parse it anyways */
                        Object[] o = (Object[]) tree.getNodeAttribute(tree.getNode(i), name);
                        double[] probabilities = new double[o.length];
                        for (int k = 0; k < o.length; k++) {
                            probabilities[k] = (Double) o[k];
                        }
                        s.setProbabilities(probabilities);
                    } else if (name.matches("states_" + d + ".set")) {
                        /* Not necessary but lets parse it anyways */
                        Object[] o = (Object[]) tree.getNodeAttribute(tree.getNode(i), name);
                        String[] set = new String[o.length];
                        for (int k = 0; k < o.length; k++) {
                            set[k] = ((String) o[k]).replaceAll("\"", "");
                        }
                        s.setSet(set);
                    }
                    //                        }
                    states.put(d, s);
                }
            }
            State[] statesArray = states.values().toArray(new State[states.size()]);
            Arrays.sort(statesArray);
            /* Set the default length to the number of characters that it would need */
            StringBuffer sb = new StringBuffer(statesArray.length * statesArray[0].getState().length());
            for (State s : statesArray) {
                sb.append(s.getState());
            }
            tree.setNodeAttribute(tree.getNode(i), "seq", sb.toString());
        }
        /* Export the new tree with the new sequences */
        TreeExporter exporter = new NexusExporter(System.out);
        exporter.exportTree(tree);
        System.out.println("Begin trees;");
        System.out.println("\ttree max_tree = " + tree.toString());
        System.out.println("End;");
    } catch (IOException e) {
        System.err.println("Error Parsing Input log: " + e.getMessage());
    } catch (Importer.ImportException e) {
        System.err.println("Error Parsing Input Tree: " + e.getMessage());
    }
}

Example 18 with Importer

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

the class SeqGen method main.

public static void main(String[] argv) {
    String treeFileName = argv[0];
    String outputFileStem = argv[1];
    int length = 500;
    double[] frequencies = new double[] { 0.25, 0.25, 0.25, 0.25 };
    double kappa = 10.0;
    double alpha = 0.5;
    double substitutionRate = argv.length < 3 ? 1.0E-3 : Double.parseDouble(argv[2]);
    int categoryCount = argv.length < 4 ? 8 : Integer.parseInt(argv[3]);
    //1.56E-6;
    double damageRate = argv.length < 5 ? 0 : Double.parseDouble(argv[4]);
    System.out.println("substitutionRate = " + substitutionRate + "; categoryCount = " + categoryCount + "; damageRate = " + damageRate);
    FrequencyModel freqModel = new FrequencyModel(dr.evolution.datatype.Nucleotides.INSTANCE, frequencies);
    HKY hkyModel = new HKY(kappa, freqModel);
    SiteModel siteModel = null;
    if (categoryCount > 1) {
        siteModel = new GammaSiteModel(hkyModel, alpha, categoryCount);
    } else {
        // no rate heterogeneity
        siteModel = new GammaSiteModel(hkyModel);
    }
    List<Tree> trees = new ArrayList<Tree>();
    FileReader reader = null;
    try {
        reader = new FileReader(treeFileName);
        //            TreeImporter importer = new NexusImporter(reader);
        TreeImporter importer = new NewickImporter(reader);
        while (importer.hasTree()) {
            Tree tree = importer.importNextTree();
            trees.add(tree);
            System.out.println("tree height = " + tree.getNodeHeight(tree.getRoot()) + "; leave nodes = " + tree.getExternalNodeCount());
        }
    } catch (FileNotFoundException e) {
        e.printStackTrace();
        return;
    } catch (Importer.ImportException e) {
        e.printStackTrace();
        return;
    } catch (IOException e) {
        e.printStackTrace();
        return;
    }
    SeqGen seqGen = new SeqGen(length, substitutionRate, freqModel, hkyModel, siteModel, damageRate);
    int i = 1;
    for (Tree tree : trees) {
        Alignment alignment = seqGen.simulate(tree);
        FileWriter writer = null;
        try {
            //                writer = new FileWriter(outputFileStem + (i < 10 ? "00" : (i < 100 ? "0" : "")) + i + ".nex");
            //                NexusExporter exporter = new NexusExporter(writer);
            //
            //                exporter.exportAlignment(alignment);
            //
            //                writer.close();
            String outputFileName = outputFileStem + "-" + substitutionRate + ".fasta";
            writer = new FileWriter(outputFileName);
            BufferedWriter bf = new BufferedWriter(writer);
            FastaExporter exporter = new FastaExporter(bf);
            exporter.exportSequences(alignment.getSequenceList());
            bf.close();
            System.out.println("Write " + i + "th sequence file : " + outputFileName);
            i++;
        } catch (IOException e) {
            e.printStackTrace();
            return;
        }
    }
}

Example 19 with Importer

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

the class KCPathDifferenceMetric method main.

public static void main(String[] args) {
    try {
        //4-taxa example
        NewickImporter importer = new NewickImporter("(('A':1.2,'B':0.8):0.5,('C':0.8,'D':1.0):1.1)");
        Tree treeOne = importer.importNextTree();
        System.out.println("4-taxa tree 1: " + treeOne);
        importer = new NewickImporter("((('A':0.8,'B':1.4):0.3,'C':0.7):0.9,'D':1.0)");
        Tree treeTwo = importer.importNextTree();
        System.out.println("4-taxa tree 2: " + treeTwo + "\n");
        ArrayList<Double> lambdaValues = new ArrayList<Double>();
        lambdaValues.add(0.0);
        lambdaValues.add(0.5);
        lambdaValues.add(1.0);
        List<Double> metric = (new KCPathDifferenceMetric().getMetric(treeOne, treeTwo, lambdaValues));
        List<Double> metric_old = (new KCPathDifferenceMetric().getMetric_old(treeOne, treeTwo, lambdaValues));
        System.out.println("\nPaired trees:");
        System.out.println("lambda (0.0) = " + metric.get(0) + " old = " + metric_old.get(0));
        System.out.println("lambda (0.5) = " + metric.get(1) + " old = " + metric_old.get(1));
        System.out.println("lambda (1.0) = " + metric.get(2) + " old = " + metric_old.get(2));
        //Additional test for comparing a collection of trees against a (fixed) focal tree
        metric = new KCPathDifferenceMetric(treeOne).getMetric(treeTwo, lambdaValues);
        metric_old = new KCPathDifferenceMetric(treeOne).getMetric_old(treeTwo, lambdaValues);
        System.out.println("\nFocal trees:");
        System.out.println("lambda (0.0) = " + metric.get(0) + " old = " + metric_old.get(0));
        System.out.println("lambda (0.5) = " + metric.get(1) + " old = " + metric_old.get(1));
        System.out.println("lambda (1.0) = " + metric.get(2) + " old = " + metric_old.get(2));
        //5-taxa example
        importer = new NewickImporter("(((('A':0.6,'B':0.6):0.1,'C':0.5):0.4,'D':0.7):0.1,'E':1.3)");
        treeOne = importer.importNextTree();
        System.out.println("5-taxa tree 1: " + treeOne);
        importer = new NewickImporter("((('A':0.8,'B':1.4):0.1,'C':0.7):0.2,('D':1.0,'E':0.9):1.3)");
        treeTwo = importer.importNextTree();
        System.out.println("5-taxa tree 2: " + treeTwo + "\n");
        //lambda = 0.0 should yield: sqrt(7) = 2.6457513110645907162
        //lambda = 1.0 should yield: sqrt(2.96) = 1.7204650534085252911
        lambdaValues = new ArrayList<Double>();
        lambdaValues.add(0.0);
        lambdaValues.add(0.5);
        lambdaValues.add(1.0);
        metric = (new KCPathDifferenceMetric().getMetric(treeOne, treeTwo, lambdaValues));
        System.out.println("\nPaired trees:");
        System.out.println("lambda (0.0) = " + metric.get(0) + " old = " + metric_old.get(0));
        System.out.println("lambda (0.5) = " + metric.get(1) + " old = " + metric_old.get(1));
        System.out.println("lambda (1.0) = " + metric.get(2) + " old = " + metric_old.get(2));
        //Additional test for comparing a collection of trees against a (fixed) focal tree
        metric = new KCPathDifferenceMetric(treeOne).getMetric(treeTwo, lambdaValues);
        System.out.println("\nFocal trees:");
        System.out.println("lambda (0.0) = " + metric.get(0) + " old = " + metric_old.get(0));
        System.out.println("lambda (0.5) = " + metric.get(1) + " old = " + metric_old.get(1));
        System.out.println("lambda (1.0) = " + metric.get(2) + " old = " + metric_old.get(2));
        //timings
        long startTime = System.currentTimeMillis();
        for (int i = 0; i < 1000000; i++) {
            new KCPathDifferenceMetric().getMetric_old(treeOne, treeTwo, lambdaValues);
        }
        System.out.println("Old algorithm: " + (System.currentTimeMillis() - startTime) + " ms");
        startTime = System.currentTimeMillis();
        for (int i = 0; i < 1000000; i++) {
            new KCPathDifferenceMetric().getMetric(treeOne, treeTwo, lambdaValues);
        }
        System.out.println("New algorithm: " + (System.currentTimeMillis() - startTime) + " ms");
    } catch (Importer.ImportException ie) {
        System.err.println(ie);
    } catch (IOException ioe) {
        System.err.println(ioe);
    }
}

Example 20 with Importer

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

the class EmpiricalTreeDistributionModelParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    final String fileName = xo.getStringAttribute(FILE_NAME);
    // default is random tree
    int startingTree = xo.getAttribute(STARTING_TREE, -1);
    // default is random draw
    boolean iterate = xo.getAttribute(ITERATE, false);
    if (iterate && startingTree < 0) {
        startingTree = 0;
    }
    Logger.getLogger("dr.evomodel").info("Creating the empirical tree distribution model, '" + xo.getId() + "'");
    TaxonList taxa = (TaxonList) xo.getChild(TaxonList.class);
    final File file = FileHelpers.getFile(fileName);
    Tree[] trees = null;
    NexusImporter importer = null;
    try {
        FileReader reader = new FileReader(file);
        importer = new NexusImporter(reader);
        if (!iterate) {
            // Re-order taxon numbers to original TaxonList order
            trees = importer.importTrees(taxa, true);
            reader.close();
        }
    } catch (FileNotFoundException e) {
        throw new XMLParseException(e.getMessage());
    } catch (IOException e) {
        throw new XMLParseException(e.getMessage());
    } catch (Importer.ImportException e) {
        throw new XMLParseException(e.getMessage());
    }
    if (iterate) {
        Logger.getLogger("dr.evomodel").info("    Iterate over each tree from file, " + fileName);
        return new EmpiricalTreeDistributionModel(importer, startingTree);
    } else {
        Logger.getLogger("dr.evomodel").info("    Randomly jump between " + trees.length + " trees from file, " + fileName);
        return new EmpiricalTreeDistributionModel(trees, startingTree);
    }
}