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

Example 56 with Taxon

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

the class PlinkImporter method addTaxonAttribute.

public void addTaxonAttribute(TaxonList inTaxonList, String traitName) {
    taxonList = new Taxa();
    for (Taxon taxon : inTaxonList) {
        List<Double> valueList = taxonHash.get(taxon.getId());
        if (valueList == null) {
            Logger.getLogger("dr.evolution").warning("Taxon " + taxon.getId() + " not found in PLINK data");
        } else {
            String string = makeStringAttribute(valueList);
            ((Taxa) taxonList).addTaxon(taxon);
            taxon.setAttribute(traitName, string);
        }
        if (DEBUG) {
            System.err.println("Added trait for " + taxon.getId());
        }
    }
}

Example 57 with Taxon

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

the class BEAUTiImporter method importTraits.

public void importTraits(final File file) throws Exception {
    List<TraitData> importedTraits = new ArrayList<TraitData>();
    Taxa taxa = options.taxonList;
    DataTable<String[]> dataTable = DataTable.Text.parse(new FileReader(file));
    String[] traitNames = dataTable.getColumnLabels();
    String[] taxonNames = dataTable.getRowLabels();
    for (int i = 0; i < dataTable.getColumnCount(); i++) {
        boolean warningGiven = false;
        String traitName = traitNames[i];
        String[] values = dataTable.getColumn(i);
        Class c = null;
        if (!isMissingValue(values[0])) {
            c = Utils.detectType(values[0]);
        }
        for (int j = 1; j < values.length; j++) {
            if (!isMissingValue(values[j])) {
                if (c == null) {
                    c = Utils.detectType(values[j]);
                } else {
                    Class c1 = Utils.detectType(values[j]);
                    if (c == Integer.class && c1 == Double.class) {
                        // change the type to double
                        c = Double.class;
                    }
                    if (c1 != c && !(c == Double.class && c1 == Integer.class) && !warningGiven) {
                        JOptionPane.showMessageDialog(frame, "Not all values of same type for trait" + traitName, "Incompatible values", JOptionPane.WARNING_MESSAGE);
                        warningGiven = true;
                    }
                }
            }
        }
        TraitData.TraitType t = (c == Boolean.class || c == String.class || c == null) ? TraitData.TraitType.DISCRETE : (c == Integer.class) ? TraitData.TraitType.INTEGER : TraitData.TraitType.CONTINUOUS;
        TraitData newTrait = new TraitData(options, traitName, file.getName(), t);
        if (validateTraitName(traitName)) {
            importedTraits.add(newTrait);
        }
        int j = 0;
        for (final String taxonName : taxonNames) {
            final int index = taxa.getTaxonIndex(taxonName);
            Taxon taxon;
            if (index >= 0) {
                taxon = taxa.getTaxon(index);
            } else {
                taxon = new Taxon(taxonName);
                taxa.addTaxon(taxon);
            }
            if (!isMissingValue(values[j])) {
                taxon.setAttribute(traitName, Utils.constructFromString(c, values[j]));
            } else {
                // AR - merge rather than replace existing trait values
                if (taxon.getAttribute(traitName) == null) {
                    taxon.setAttribute(traitName, "?");
                }
            }
            j++;
        }
    }
    setData(file.getName(), taxa, null, null, null, importedTraits, null);
}

Example 58 with Taxon

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

the class BEAUTiImporter method checkTaxonList.

private void checkTaxonList(TaxonList taxonList) throws ImportException {
    // check the taxon names for invalid characters
    boolean foundAmp = false;
    for (Taxon taxon : taxonList) {
        String name = taxon.getId();
        if (name.indexOf('&') >= 0) {
            foundAmp = true;
        }
    }
    if (foundAmp) {
        throw new ImportException("One or more taxon names include an illegal character ('&').\n" + "These characters will prevent BEAST from reading the resulting XML file.\n\n" + "Please edit the taxon name(s) before reloading the data file.");
    }
    // make sure they all have dates...
    for (int i = 0; i < taxonList.getTaxonCount(); i++) {
        if (taxonList.getTaxonAttribute(i, "date") == null) {
            Date origin = new Date(0);
            dr.evolution.util.Date date = dr.evolution.util.Date.createTimeSinceOrigin(0.0, Units.Type.YEARS, origin);
            taxonList.getTaxon(i).setAttribute("date", date);
        }
    }
}

Example 59 with Taxon

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

the class FastaImporter method importAlignment.

/**
     * importAlignment.
     */
public Alignment importAlignment() throws IOException, ImportException {
    SimpleAlignment alignment = null;
    try {
        // find fasta line start
        while (read() != FASTA_FIRST_CHAR) {
        }
        do {
            final String name = readLine().trim();
            StringBuffer seq = new StringBuffer();
            readSequence(seq, dataType, "" + FASTA_FIRST_CHAR, Integer.MAX_VALUE, "-", "?", "", "");
            if (alignment == null) {
                alignment = new SimpleAlignment();
            }
            alignment.addSequence(new Sequence(new Taxon(name.toString()), seq.toString()));
        } while (getLastDelimiter() == FASTA_FIRST_CHAR);
    } catch (EOFException e) {
    // catch end of file the ugly way.
    }
    return alignment;
}

Example 60 with Taxon

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

the class PLCoalescentSimulator method main.

public static void main(String[] arg) throws IOException {
    // READ DEMOGRAPHIC FUNCTION
    String filename = arg[0];
    BufferedReader reader = new BufferedReader(new FileReader(filename));
    double popSizeScale = 1.0;
    double generationTime = 1.0;
    if (arg.length > 2) {
        popSizeScale = Double.parseDouble(arg[2]);
    }
    if (arg.length > 3) {
        generationTime = Double.parseDouble(arg[3]);
    }
    PrintWriter populationFuncLogger = null;
    if (arg.length > 5) {
        String logFileName = arg[5];
        if (logFileName.equals("-")) {
            populationFuncLogger = new PrintWriter(System.out);
        } else {
            populationFuncLogger = new PrintWriter(new FileWriter(logFileName));
        }
    }
    List<Double> times = new ArrayList<Double>();
    String line = reader.readLine();
    String[] tokens = line.trim().split("[\t ]+");
    if (tokens.length < 2)
        throw new RuntimeException();
    ArrayList<ArrayList> popSizes = new ArrayList<ArrayList>();
    while (line != null) {
        double time = Double.parseDouble(tokens[0]) / generationTime;
        times.add(time);
        for (int i = 1; i < tokens.length; i++) {
            popSizes.add(new ArrayList<Double>());
            popSizes.get(i - 1).add(Double.parseDouble(tokens[i]));
        }
        line = reader.readLine();
        if (line != null) {
            tokens = line.trim().split("[\t ]+");
            if (tokens.length != popSizes.size() + 1)
                throw new RuntimeException();
        }
    }
    reader.close();
    // READ SAMPLE TIMES
    String samplesFilename = arg[1];
    reader = new BufferedReader(new FileReader(samplesFilename));
    line = reader.readLine();
    Taxa taxa = new Taxa();
    int id = 0;
    while (line != null) {
        if (!line.startsWith("#")) {
            tokens = line.split("[\t ]+");
            if (tokens.length == 4) {
                double t0 = Double.parseDouble(tokens[0]);
                double t1 = Double.parseDouble(tokens[1]);
                double dt = Double.parseDouble(tokens[2]);
                int k = Integer.parseInt(tokens[3]);
                for (double time = t0; time <= t1; time += dt) {
                    double sampleTime = time / generationTime;
                    for (int i = 0; i < k; i++) {
                        Taxon taxon = new Taxon("t" + id);
                        taxon.setAttribute(dr.evolution.util.Date.DATE, new Date(sampleTime, Units.Type.GENERATIONS, true));
                        taxa.addTaxon(taxon);
                        id += 1;
                    }
                }
            } else {
                // sample times are in the same units as simulation
                double sampleTime = Double.parseDouble(tokens[0]) / generationTime;
                int count = Integer.parseInt(tokens[1]);
                for (int i = 0; i < count; i++) {
                    Taxon taxon = new Taxon(id + "");
                    taxon.setAttribute(dr.evolution.util.Date.DATE, new Date(sampleTime, Units.Type.GENERATIONS, true));
                    taxa.addTaxon(taxon);
                    id += 1;
                }
            }
        }
        line = reader.readLine();
    }
    double minTheta = Double.MAX_VALUE;
    double maxTheta = 0.0;
    PrintWriter out;
    if (arg.length > 4) {
        out = new PrintWriter(new FileWriter(arg[4]));
    } else {
        out = new PrintWriter(System.out);
    }
    int pp = 0;
    for (List<Double> popSize : popSizes) {
        double[] thetas = new double[popSize.size()];
        double[] intervals = new double[times.size() - 1];
        if (populationFuncLogger != null) {
            populationFuncLogger.println("# " + pp);
            ++pp;
        }
        // must reverse the direction of the model
        for (int j = intervals.length; j > 0; j--) {
            intervals[intervals.length - j] = times.get(j) - times.get(j - 1);
            final double theta = popSize.get(j) * popSizeScale;
            thetas[intervals.length - j] = theta;
            if (theta < minTheta) {
                minTheta = theta;
            }
            if (theta > maxTheta) {
                maxTheta = theta;
            }
            final double t = times.get(intervals.length) - times.get(j);
            if (populationFuncLogger != null) {
                populationFuncLogger.println(t + "\t" + theta);
            }
        }
        if (debug != null) {
            debug.println("min theta = " + minTheta);
            debug.println("max theta = " + maxTheta);
        }
        PiecewiseLinearPopulation demo = new PiecewiseLinearPopulation(intervals, thetas, Units.Type.GENERATIONS);
        CoalescentSimulator simulator = new CoalescentSimulator();
        Tree tree = simulator.simulateTree(taxa, demo);
        out.println(TreeUtils.newick(tree));
        if (debug != null) {
            debug.println(TreeUtils.newick(tree));
        }
    }
    if (populationFuncLogger != null) {
        populationFuncLogger.flush();
        populationFuncLogger.close();
    }
    out.flush();
    out.close();
}