Examples with Microsatellite dr.evolution.datatype.Microsatellite used on opensource projects

Example 11 with Microsatellite

use of dr.evolution.datatype.Microsatellite in project beast-mcmc by beast-dev.

the class MsatBMAParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    //get microsatellite data type
    Microsatellite dataType = (Microsatellite) xo.getChild(Microsatellite.class);
    //whether mutational bias is in logit space
    boolean logit = xo.getAttribute(LOGIT, true);
    XMLObject modelsXO = xo.getChild(MODELS);
    int modelCount = modelsXO.getChildCount();
    HashMap<Integer, Integer> modelBitIndMap = new HashMap<Integer, Integer>(modelCount);
    for (int i = 0; i < modelCount; i++) {
        XMLObject modelXO = (XMLObject) modelsXO.getChild(i);
        String bitVec = modelXO.getStringAttribute(BINARY);
        int bitVecVal = Integer.parseInt(bitVec, 2);
        int modelCode = modelXO.getIntegerAttribute(CODE);
        modelBitIndMap.put(bitVecVal, modelCode);
    }
    Parameter[][] paramModelMap = new Parameter[6][modelCount];
    XMLObject propRatesXO = xo.getChild(RATE_PROPS);
    ArrayList<Parameter> rateProps = processParameters(propRatesXO, paramModelMap, MsatBMA.PROP_INDEX);
    XMLObject quadRatesXO = xo.getChild(RATE_QUADS);
    ArrayList<Parameter> rateQuads = processParameters(quadRatesXO, paramModelMap, MsatBMA.QUAD_INDEX);
    XMLObject biasConstsXO = xo.getChild(BIAS_CONSTS);
    ArrayList<Parameter> biasConsts = processParameters(biasConstsXO, paramModelMap, MsatBMA.BIAS_CONST_INDEX);
    XMLObject biasLinsXO = xo.getChild(BIAS_LINS);
    ArrayList<Parameter> biasLins = processParameters(biasLinsXO, paramModelMap, MsatBMA.BIAS_LIN_INDEX);
    XMLObject geosXO = xo.getChild(GEOS);
    ArrayList<Parameter> geos = processParameters(geosXO, paramModelMap, MsatBMA.GEO_INDEX);
    XMLObject phaseProbXO = xo.getChild(PHASE_PROBS);
    ArrayList<Parameter> phaseProbs = processParameters(phaseProbXO, paramModelMap, MsatBMA.PHASE_PROB_INDEX);
    Parameter modelChoose = (Parameter) xo.getElementFirstChild(MODEL_CHOOSE);
    Parameter modelIndicator = (Parameter) xo.getElementFirstChild(MODEL_INDICATOR);
    printParameters(paramModelMap);
    return new MsatBMA(dataType, logit, rateProps, rateQuads, biasConsts, biasLins, geos, phaseProbs, paramModelMap, modelChoose, modelIndicator, modelBitIndMap);
}

Example 12 with Microsatellite

use of dr.evolution.datatype.Microsatellite in project beast-mcmc by beast-dev.

the class NewMicrosatelliteModelParser method parseXMLObject.

//AbstractXMLObjectParser implementation
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    //get msat data type
    System.out.println("Using watkins' model");
    Microsatellite msat = (Microsatellite) xo.getChild(Microsatellite.class);
    //get FrequencyModel
    FrequencyModel freqModel = null;
    if (xo.hasChildNamed(FrequencyModelParser.FREQUENCIES)) {
        freqModel = (FrequencyModel) xo.getElementFirstChild(FrequencyModelParser.FREQUENCIES);
    }
    return new NewMicrosatelliteModel(msat, freqModel);
}

Example 13 with Microsatellite

use of dr.evolution.datatype.Microsatellite in project beast-mcmc by beast-dev.

the class BeautiOptions method unshareMicroSat.

public void unshareMicroSat() {
    Microsatellite microsatellite = null;
    for (PartitionSubstitutionModel model : getPartitionSubstitutionModels(Microsatellite.INSTANCE)) {
        if (microsatellite == null) {
            microsatellite = model.getMicrosatellite();
        } else {
            microsatellite = new Microsatellite(model.getName() + ".microsat", microsatellite.getMin(), microsatellite.getMax(), 1);
            model.setMicrosatellite(microsatellite);
        }
    }
}

Example 14 with Microsatellite

use of dr.evolution.datatype.Microsatellite in project beast-mcmc by beast-dev.

the class TwoPhaseModelParser method parseXMLObject.

//AbstractXMLObjectParser implementation
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    OnePhaseModel subModel = (OnePhaseModel) xo.getElementFirstChild(SUBMODEL);
    Microsatellite dataType = (Microsatellite) xo.getChild(Microsatellite.class);
    Parameter.Default geoParam = (Parameter.Default) xo.getElementFirstChild(GEO_PARAM);
    Parameter paramP = (Parameter) xo.getElementFirstChild(ONEPHASEPR_PARAM);
    Parameter limitE = null;
    if (xo.hasChildNamed(TRANS_PARAM)) {
        limitE = (Parameter) xo.getElementFirstChild(TRANS_PARAM);
    }
    boolean estimateSubmodelParams = xo.getAttribute(ESTIMATE_SUBMODEL_PARAMS, false);
    FrequencyModel freqModel = null;
    if (xo.hasChildNamed(FrequencyModelParser.FREQUENCIES)) {
        freqModel = (FrequencyModel) xo.getElementFirstChild(FrequencyModelParser.FREQUENCIES);
    }
    return new TwoPhaseModel(dataType, freqModel, subModel, paramP, geoParam, limitE, estimateSubmodelParams);
}

Example 15 with Microsatellite

use of dr.evolution.datatype.Microsatellite 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;
}