Examples with Taxon dr.evolution.util.Taxon used on opensource projects

Example 91 with Taxon

use of dr.evolution.util.Taxon in project beast-mcmc by beast-dev.

the class FitchParsimony method main.

public static void main(String[] argv) {
    FlexibleNode tip1 = new FlexibleNode(new Taxon("tip1"));
    FlexibleNode tip2 = new FlexibleNode(new Taxon("tip2"));
    FlexibleNode tip3 = new FlexibleNode(new Taxon("tip3"));
    FlexibleNode tip4 = new FlexibleNode(new Taxon("tip4"));
    FlexibleNode tip5 = new FlexibleNode(new Taxon("tip5"));
    FlexibleNode node1 = new FlexibleNode();
    node1.addChild(tip1);
    node1.addChild(tip2);
    FlexibleNode node2 = new FlexibleNode();
    node2.addChild(tip4);
    node2.addChild(tip5);
    FlexibleNode node3 = new FlexibleNode();
    node3.addChild(tip3);
    node3.addChild(node2);
    FlexibleNode root = new FlexibleNode();
    root.addChild(node1);
    root.addChild(node3);
    FlexibleTree tree = new FlexibleTree(root);
    Patterns patterns = new Patterns(Nucleotides.INSTANCE, tree);
    patterns.addPattern(new int[] { 1, 0, 1, 2, 2 });
    FitchParsimony fitch = new FitchParsimony(patterns, false);
    System.out.println("No. Steps = " + fitch.getScore(tree));
    System.out.println(" state(node1) = " + fitch.getStates(tree, node1)[0]);
    System.out.println(" state(node2) = " + fitch.getStates(tree, node2)[0]);
    System.out.println(" state(node3) = " + fitch.getStates(tree, node3)[0]);
    System.out.println(" state(root) = " + fitch.getStates(tree, root)[0]);
    System.out.println("\nParsimony static methods:");
    System.out.println("No. Steps = " + Parsimony.getParsimonySteps(tree, patterns));
    Parsimony.reconstructParsimonyStates(tree, patterns);
    System.out.println(" state(node1) = " + tree.getNodeAttribute(node1, "rstate1"));
    System.out.println(" state(node2) = " + tree.getNodeAttribute(node2, "rstate1"));
    System.out.println(" state(node3) = " + tree.getNodeAttribute(node3, "rstate1"));
    System.out.println(" state(root) = " + tree.getNodeAttribute(root, "rstate1"));
}

Example 92 with Taxon

use of dr.evolution.util.Taxon in project beast-mcmc by beast-dev.

the class SankoffParsimony method main.

public static void main(String[] argv) {
    FlexibleNode tip1 = new FlexibleNode(new Taxon("tip1"));
    FlexibleNode tip2 = new FlexibleNode(new Taxon("tip2"));
    FlexibleNode tip3 = new FlexibleNode(new Taxon("tip3"));
    FlexibleNode tip4 = new FlexibleNode(new Taxon("tip4"));
    FlexibleNode tip5 = new FlexibleNode(new Taxon("tip5"));
    FlexibleNode node1 = new FlexibleNode();
    node1.addChild(tip1);
    node1.addChild(tip2);
    FlexibleNode node2 = new FlexibleNode();
    node2.addChild(tip4);
    node2.addChild(tip5);
    FlexibleNode node3 = new FlexibleNode();
    node3.addChild(tip3);
    node3.addChild(node2);
    FlexibleNode root = new FlexibleNode();
    root.addChild(node1);
    root.addChild(node3);
    FlexibleTree tree = new FlexibleTree(root);
    Patterns patterns = new Patterns(Nucleotides.INSTANCE, tree);
    //patterns.addPattern(new int[] {1, 0, 1, 2, 2});
    //patterns.addPattern(new int[] {2, 1, 1, 1, 2});
    patterns.addPattern(new int[] { 2, 3, 1, 3, 3 });
    FitchParsimony fitch = new FitchParsimony(patterns, false);
    SankoffParsimony sankoff = new SankoffParsimony(patterns);
    for (int i = 0; i < patterns.getPatternCount(); i++) {
        double[] scores = fitch.getSiteScores(tree);
        System.out.println("Pattern = " + i);
        System.out.println("Fitch:");
        System.out.println("  No. Steps = " + scores[i]);
        System.out.println("    state(node1) = " + fitch.getStates(tree, node1)[i]);
        System.out.println("    state(node2) = " + fitch.getStates(tree, node2)[i]);
        System.out.println("    state(node3) = " + fitch.getStates(tree, node3)[i]);
        System.out.println("    state(root) = " + fitch.getStates(tree, root)[i]);
        scores = sankoff.getSiteScores(tree);
        System.out.println("Sankoff:");
        System.out.println("  No. Steps = " + scores[i]);
        System.out.println("    state(node1) = " + sankoff.getStates(tree, node1)[i]);
        System.out.println("    state(node2) = " + sankoff.getStates(tree, node2)[i]);
        System.out.println("    state(node3) = " + sankoff.getStates(tree, node3)[i]);
        System.out.println("    state(root) = " + sankoff.getStates(tree, root)[i]);
        System.out.println();
    }
}

Example 93 with Taxon

use of dr.evolution.util.Taxon in project beast-mcmc by beast-dev.

the class MicroSatImporter method importPatterns.

public List<Patterns> importPatterns() throws IOException, Importer.ImportException {
    List<Patterns> microsatPatList = new ArrayList<Patterns>();
    // 1st List<String> is taxon names
    List<List<String>> data = new ArrayList<List<String>>();
    // microsatName[0] is keyword, microsatName[1] is name
    String[] microsatName = new String[2];
    microsatName[1] = "unnamed.microsat";
    String line = reader.readLine();
    while (line.startsWith("#")) {
        // comments
        if (line.toUpperCase().contains("NAME")) {
            microsatName = line.trim().split("[" + delimiter + " ]+");
            if (microsatName[1] == null || microsatName[1].length() < 1)
                throw new Importer.ImportException("Improper microsatellite name : " + microsatName[1]);
        }
        line = reader.readLine();
    }
    // read locus (microsat pattern) names in the 1st row after comments, where 1st element is id
    // trim trailing whitespace ?
    String[] names = line.trim().split("[" + delimiter + " ]+");
    // for validation
    int colLen = names.length;
    if (colLen < 2)
        throw new Importer.ImportException("Import file must have more than 1 columns : " + colLen);
    for (int i = 0; i < colLen; i++) {
        // init data
        List<String> l = new ArrayList<String>();
        data.add(l);
    }
    int min = Integer.MAX_VALUE;
    int max = Integer.MIN_VALUE;
    line = reader.readLine();
    while (line != null) {
        // read data
        String[] dataLine = line.trim().split("[" + delimiter + " ]+");
        if (dataLine.length != colLen)
            throw new Importer.ImportException("The number of name columns are different with values columns," + "\nplease use only letters or numbers in the name.");
        for (int i = 0; i < dataLine.length; i++) {
            data.get(i).add(dataLine[i]);
            if (i > 0) {
                int v = parseInt(dataLine[i]);
                if (v != Microsatellite.UNKNOWN_STATE_LENGTH) {
                    if (min > v)
                        min = v;
                    if (max < v)
                        max = v;
                }
            }
        }
        line = reader.readLine();
    }
    if (max < min)
        throw new Importer.ImportException("Importing invalid data: max < min !");
    //        if (min - 2 < 0) throw new Importer.ImportException("Importing invaild data: min-2 < 0 where min = " + min);
    // The min also = 1 and max should be the longest repeat length + 2.
    microsatellite = new Microsatellite(microsatName[1], 1, max + 2, 1);
    Taxa taxaHaploid = new Taxa();
    for (String name : data.get(0)) {
        Taxon t = new Taxon(name);
        taxaHaploid.addTaxon(t);
    }
    //        unionSetTaxonList.addTaxa(taxaHaploid);
    Patterns microsatPat;
    for (int i = 1; i < data.size(); i++) {
        // create pattern
        //            List<Integer> pattern = new ArrayList<Integer>();
        List<Integer> pattern;
        Taxa taxa = new Taxa();
        if ((i + 1 < data.size()) && names[i].equalsIgnoreCase(names[i + 1])) {
            // diploid: Locus2	Locus2
            Taxa taxaDiploid = new Taxa();
            for (String name : data.get(0)) {
                Taxon t = new Taxon(names[i] + "_1_" + name);
                taxaDiploid.addTaxon(t);
            }
            for (String name : data.get(0)) {
                Taxon t = new Taxon(names[i] + "_2_" + name);
                taxaDiploid.addTaxon(t);
            }
            if (unionSetTaxonList.containsAny(taxaDiploid))
                throw new Importer.ImportException("Importing invalid data: duplicate taxon name in this locus : " + names[i]);
            unionSetTaxonList.addTaxa(taxaDiploid);
            hasDifferentTaxon = true;
            pattern = new ArrayList<Integer>();
            String value;
            int size = data.get(i).size();
            for (int v = 0; v < size; v++) {
                value = data.get(i).get(v);
                //                    if (!isUnknownChar(value)) {
                Taxon t = taxaDiploid.getTaxon(v);
                if (!taxa.contains(t)) {
                    taxa.addTaxon(t);
                    //microsatellite.getState(value);
                    pattern.add(parseInt(value));
                    if (!unionSetTaxonList.contains(t)) {
                        unionSetTaxonList.addTaxon(t);
                        if (i > 1)
                            hasDifferentTaxon = true;
                    }
                }
            //                    }
            }
            for (int v = 0; v < data.get(i + 1).size(); v++) {
                value = data.get(i + 1).get(v);
                //                    if (!isUnknownChar(value)) {
                Taxon t = taxaDiploid.getTaxon(v + size);
                if (!taxa.contains(t)) {
                    taxa.addTaxon(t);
                    //microsatellite.getState(value);
                    pattern.add(parseInt(value));
                    if (!unionSetTaxonList.contains(t)) {
                        unionSetTaxonList.addTaxon(t);
                        if (i > 1)
                            hasDifferentTaxon = true;
                    }
                }
            //                    }
            }
            i++;
        } else {
            // haploid Locus1
            pattern = new ArrayList<Integer>();
            for (int v = 0; v < data.get(i).size(); v++) {
                String value = data.get(i).get(v);
                //                    if (!isUnknownChar(value)) {
                Taxon t = taxaHaploid.getTaxon(v);
                if (!taxa.contains(t)) {
                    taxa.addTaxon(t);
                    //microsatellite.getState(value);
                    pattern.add(parseInt(value));
                    if (!unionSetTaxonList.contains(t)) {
                        unionSetTaxonList.addTaxon(t);
                        if (i > 1)
                            hasDifferentTaxon = true;
                    }
                }
            //                    }
            }
        }
        int[] p = new int[pattern.size()];
        for (int v = 0; v < pattern.size(); v++) {
            p[v] = pattern.get(v);
        }
        microsatPat = new Patterns(microsatellite, taxa);
        microsatPat.addPattern(p);
        microsatPat.setId(names[i]);
        microsatPatList.add(microsatPat);
    }
    return microsatPatList;
}

Example 94 with Taxon

use of dr.evolution.util.Taxon in project beast-mcmc by beast-dev.

the class PhylipSequentialImporter method importAlignment.

/**
	 * importAlignment. 
	 */
public Alignment importAlignment() throws IOException, Importer.ImportException {
    SimpleAlignment alignment = null;
    try {
        int taxonCount = readInteger();
        int siteCount = readInteger();
        String firstSeq = null;
        for (int i = 0; i < taxonCount; i++) {
            StringBuffer name = new StringBuffer();
            char ch = read();
            int n = 0;
            while (!Character.isWhitespace(ch) && (maxNameLength < 1 || n < maxNameLength)) {
                name.append(ch);
                ch = read();
                n++;
            }
            StringBuffer seq = new StringBuffer(siteCount);
            readSequence(seq, dataType, "", siteCount, "-", "?", ".", firstSeq);
            if (firstSeq == null) {
                firstSeq = seq.toString();
            }
            if (alignment == null) {
                alignment = new SimpleAlignment();
            }
            alignment.addSequence(new Sequence(new Taxon(name.toString()), seq.toString()));
        }
    } catch (EOFException e) {
    }
    return alignment;
}

Example 95 with Taxon

use of dr.evolution.util.Taxon in project beast-mcmc by beast-dev.

the class NewickImporter method readExternalNode.

/**
     * Reads an external node in.
     */
private FlexibleNode readExternalNode(TaxonList taxonList) throws IOException, ImportException {
    FlexibleNode node = new FlexibleNode();
    String label = readToken(":(),;");
    Taxon taxon;
    if (taxonList != null) {
        // if a taxon list is given then the taxon must be in it...
        int index = taxonList.getTaxonIndex(label);
        if (index != -1) {
            taxon = taxonList.getTaxon(index);
        } else {
            throw new UnknownTaxonException("Taxon in tree, '" + label + "' is unknown");
        }
    } else {
        // No taxon list given so create new taxa
        taxon = new Taxon(label);
    }
    node.setTaxon(taxon);
    return node;
}