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

Example 6 with NexusImporter

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

the class SpeciesDelimitationAnalyser method readtrees.

void readtrees() throws IOException {
    clusters = new ArrayList<Cluster>(0);
    int totalTrees;
    FileReader fileReader = new FileReader(inputFileName);
    NexusImporter importer = new NexusImporter(fileReader);
    System.out.println("Reading trees...");
    try {
        taxonList = importer.parseTaxaBlock();
        totalTrees = 0;
        while (importer.hasTree()) {
            Tree tree = importer.importNextTree();
            if (totalTrees >= burnin) {
                Cluster sd = new Cluster(taxonList, tree, collapseheight);
                clusters.add(sd);
            }
            if (totalTrees > 0 && (totalTrees % 100 == 0)) {
                System.out.print("*");
                System.out.flush();
            }
            if (totalTrees > 0 && (totalTrees % 5000 == 0)) {
                System.out.println(" " + totalTrees);
                System.out.flush();
            }
            totalTrees++;
        }
        System.out.println("");
    } catch (Importer.ImportException e) {
        System.err.println("Error Parsing Input Tree: " + e.getMessage());
        return;
    }
    fileReader.close();
    if (totalTrees < 1) {
        System.err.println("No trees");
        return;
    }
    System.out.println("Total trees read: " + totalTrees);
}

Example 7 with NexusImporter

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

the class NodeStateAnalyser 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 mrsd, double scale) {
    int count = 0;
    Map<String, List<Double>> heightMap = new HashMap<String, List<Double>>();
    Set<String> states = new TreeSet<String>();
    try {
        FileReader fileReader = new FileReader(new File(name));
        TreeImporter importer = new NexusImporter(fileReader);
        while (importer.hasTree()) {
            Tree tree = importer.importNextTree();
            if (count >= burnin) {
                for (int i = 0; i < tree.getInternalNodeCount(); i++) {
                    NodeRef node = tree.getInternalNode(i);
                    Object value = tree.getNodeAttribute(node, "state");
                    if (value != null) {
                        String state = value.toString();
                        List<Double> heights = heightMap.get(state);
                        if (heights == null) {
                            heights = new ArrayList<Double>();
                            heightMap.put(state, heights);
                            states.add(state);
                        }
                        double h = tree.getNodeHeight(node) * scale;
                        if (Double.isNaN(mrsd)) {
                            heights.add(h);
                        } else {
                            heights.add(mrsd - h);
                        }
                    } else {
                        System.out.println("Node missing state");
                    }
                }
            }
            count++;
        }
        boolean first = true;
        int maxCount = 0;
        for (String state : states) {
            if (first) {
                first = false;
            } else {
                System.out.print("\t");
            }
            System.out.print(state);
            List<Double> heights = heightMap.get(state);
            if (heights.size() > maxCount) {
                maxCount = heights.size();
            }
        }
        System.out.println();
        for (int i = 0; i < maxCount; i++) {
            first = true;
            for (String state : states) {
                if (first) {
                    first = false;
                } else {
                    System.out.print("\t");
                }
                List<Double> heights = heightMap.get(state);
                if (i < heights.size()) {
                    System.out.print(heights.get(i));
                }
            }
            System.out.println();
        }
    } 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 8 with NexusImporter

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

the class PatristicDistanceMatrix method main.

public static void main(String[] args) throws IOException, Importer.ImportException {
    File file = new File(args[0]);
    File outFile = new File(args[1]);
    PrintWriter writer = new PrintWriter(new FileWriter(outFile));
    NexusImporter importer = new NexusImporter(new FileReader(file));
    Tree[] trees = importer.importTrees(null);
    System.out.println("Found " + trees.length + " trees.");
    for (Tree tree : trees) {
        PatristicDistanceMatrix matrix = new PatristicDistanceMatrix(tree);
        writer.println(matrix.toString());
    }
    writer.flush();
    writer.close();
}

Example 9 with NexusImporter

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

the class Defects method readNexusFile.

/**
     * @param fileName
     * @throws java.io.IOException
     */
private static Alignment readNexusFile(String fileName) throws java.io.IOException {
    Alignment alignment = null;
    TaxonList taxonList = null;
    try {
        FileReader reader = new FileReader(fileName);
        NexusImporter importer = new NexusImporter(reader);
        boolean done = false;
        while (!done) {
            try {
                NexusImporter.NexusBlock block = importer.findNextBlock();
                if (block == NexusImporter.TAXA_BLOCK) {
                    if (taxonList != null) {
                        throw new NexusImporter.MissingBlockException("TAXA block already defined");
                    }
                    taxonList = importer.parseTaxaBlock();
                } else if (block == NexusImporter.DATA_BLOCK) {
                    // A data block doesn't need a taxon block before it
                    // but if one exists then it will use it.
                    alignment = importer.parseDataBlock(taxonList);
                    if (taxonList == null) {
                        taxonList = alignment;
                    }
                } else if (block == NexusImporter.TREES_BLOCK) {
                // ignore tree block
                } else {
                // Ignore the block..
                }
            } catch (EOFException ex) {
                done = true;
            }
        }
    } catch (Importer.ImportException ime) {
        System.err.println("Error reading alignment: " + ime);
    }
    return alignment;
}

Example 10 with NexusImporter

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

the class Coevolve method readNexusFile.

/**
     * @param fileName
     * @throws java.io.IOException
     */
private Alignment readNexusFile(String fileName) throws java.io.IOException {
    Alignment alignment = null;
    TaxonList taxonList = null;
    try {
        FileReader reader = new FileReader(fileName);
        NexusImporter importer = new NexusImporter(reader);
        boolean done = false;
        while (!done) {
            try {
                NexusImporter.NexusBlock block = importer.findNextBlock();
                if (block == NexusImporter.TAXA_BLOCK) {
                    if (taxonList != null) {
                        throw new NexusImporter.MissingBlockException("TAXA block already defined");
                    }
                    taxonList = importer.parseTaxaBlock();
                } else if (block == NexusImporter.DATA_BLOCK) {
                    // A data block doesn't need a taxon block before it
                    // but if one exists then it will use it.
                    alignment = importer.parseDataBlock(taxonList);
                    if (taxonList == null) {
                        taxonList = alignment;
                    }
                } else if (block == NexusImporter.TREES_BLOCK) {
                // ignore tree block
                } else {
                // Ignore the block..
                }
            } catch (EOFException ex) {
                done = true;
            }
        }
    } catch (Importer.ImportException ime) {
        System.err.println("Error reading alignment: " + ime);
    }
    return alignment;
}