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

Example 26 with NexusImporter

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

the class ConditionalCladeFrequency method report.

/**
     * Creates the report. The estimated posterior of the given tree is printed.
     *
     * @throws IOException if general I/O error occurs
     */
public void report(Reader r) throws IOException, Importer.ImportException {
    System.err.println("making report");
    ArrayList<Tree> referenceTrees = new ArrayList<Tree>();
    BufferedReader reader = new BufferedReader(r);
    String line = reader.readLine();
    if (line.toUpperCase().startsWith("#NEXUS")) {
        NexusImporter importer = new NexusImporter(reader);
        Tree[] trees = importer.importTrees(null);
        for (Tree tree : trees) {
            referenceTrees.add(tree);
            SimpleTree sTree = new SimpleTree(tree);
            System.out.println("Estimated marginal posterior by condiational clade frequencies:");
            System.out.println(getTreeProbability(sTree) + "\t\t" + sTree);
        }
    } else {
        throw new RuntimeException("Could not read reference tree. Only Nexus format is supported.");
    }
    System.out.flush();
}

Example 27 with NexusImporter

use of dr.evolution.io.NexusImporter 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);
    }
}

Example 28 with NexusImporter

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

the class AlignmentScore method main.

public static void main(String[] args) throws java.io.IOException, Importer.ImportException {
    NexusImporter importer = new NexusImporter(new FileReader(args[0]));
    Alignment alignment = importer.importAlignment();
    ExtractPairs pairs = new ExtractPairs(alignment);
    Parameter muParam = new Parameter.Default(1.0);
    Parameter kappaParam = new Parameter.Default(1.0);
    kappaParam.addBounds(new Parameter.DefaultBounds(100.0, 0.0, 1));
    muParam.addBounds(new Parameter.DefaultBounds(1.0, 1.0, 1));
    Parameter freqParam = new Parameter.Default(alignment.getStateFrequencies());
    FrequencyModel freqModel = new FrequencyModel(Nucleotides.INSTANCE, freqParam);
    SubstitutionModel substModel = new HKY(kappaParam, freqModel);
    SiteModel siteModel = new GammaSiteModel(substModel, muParam, null, 1, null);
    ScoreMatrix scoreMatrix = new ScoreMatrix(siteModel, 0.1);
    double threshold = 0.1;
    List<PairDistance> pairDistances = new ArrayList<PairDistance>();
    Set<Integer> sequencesUsed = new HashSet<Integer>();
    List<Integer> allGaps = new ArrayList<Integer>();
    for (int i = 0; i < alignment.getSequenceCount(); i++) {
        for (int j = i + 1; j < alignment.getSequenceCount(); j++) {
            Alignment pairAlignment = pairs.getPairAlignment(i, j);
            if (pairAlignment != null) {
                SitePatterns patterns = new SitePatterns(pairAlignment);
                double distance = getGeneticDistance(scoreMatrix, patterns);
                if (distance < threshold) {
                    List gaps = new ArrayList();
                    GapUtils.getGapSizes(pairAlignment, gaps);
                    pairDistances.add(new PairDistance(i, j, distance, gaps, pairAlignment.getSiteCount()));
                    System.out.print(".");
                } else {
                    System.out.print("*");
                }
            } else {
                System.out.print("x");
            }
        }
        System.out.println();
    }
    Collections.sort(pairDistances);
    int totalLength = 0;
    for (PairDistance pairDistance : pairDistances) {
        Integer x = pairDistance.x;
        Integer y = pairDistance.y;
        if (!sequencesUsed.contains(x) && !sequencesUsed.contains(y)) {
            allGaps.addAll(pairDistance.gaps);
            sequencesUsed.add(x);
            sequencesUsed.add(y);
            System.out.println("Added pair (" + x + "," + y + ") d=" + pairDistance.distance + " L=" + pairDistance.alignmentLength);
            totalLength += pairDistance.alignmentLength;
        }
    }
    printFrequencyTable(allGaps);
    System.out.println("total length=" + totalLength);
}

Example 29 with NexusImporter

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

the class TestParsimony method main.

public static void main(String[] args) throws Exception {
    // read alignments
    NexusImporter importer = new NexusImporter(new FileReader(alignmentFileName));
    Alignment alignment = importer.importAlignment();
    // alignment = new GapStrippedAlignment(alignment);
    // read trees
    Tree tree = null;
    importer = new NexusImporter(new FileReader(treeFileName));
    try {
        tree = importer.importTree(alignment);
    //((FlexibleTree)tree).resolveTree();
    } catch (Exception e) {
        System.err.println("Exception attempting to read tree: " + e.getMessage());
        System.exit(0);
    }
    //testParsimony(new FitchParsimony(alignment, false), alignment, tree);
    System.out.println("single:");
    testParsimony(new SankoffParsimony(alignment), alignment, tree);
    System.out.println("paired:");
    testPairedSites(alignment, tree);
}