Examples with Patterns dr.evolution.alignment.Patterns used on opensource projects

Example 6 with Patterns

use of dr.evolution.alignment.Patterns in project beast-mcmc by beast-dev.

the class MicrosatelliteSamplerTreeModelParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    TreeModel tree = (TreeModel) xo.getElementFirstChild(TREE);
    Parameter internalVal = (Parameter) xo.getElementFirstChild(INTERNAL_VALUES);
    Patterns microsatellitePattern = (Patterns) xo.getElementFirstChild(EXTERNAL_VALUES);
    int[] externalValues = microsatellitePattern.getPattern(0);
    HashMap<String, Integer> taxaMap = new HashMap<String, Integer>(externalValues.length);
    boolean internalValuesProvided = false;
    if (xo.hasAttribute(USE_PROVIDED_INTERNAL_VALUES)) {
        internalValuesProvided = xo.getBooleanAttribute(USE_PROVIDED_INTERNAL_VALUES);
    }
    for (int i = 0; i < externalValues.length; i++) {
        taxaMap.put(microsatellitePattern.getTaxonId(i), i);
    }
    String modelId = xo.getAttribute("id", "treeMicrosatelliteSamplerModel");
    return new MicrosatelliteSamplerTreeModel(modelId, tree, internalVal, microsatellitePattern, externalValues, taxaMap, internalValuesProvided);
}

Example 7 with Patterns

use of dr.evolution.alignment.Patterns in project beast-mcmc by beast-dev.

the class OldTreesPanel method createTree.

private void createTree() {
    if (generateTreeDialog == null) {
        generateTreeDialog = new GenerateTreeDialog(frame);
    }
    int result = generateTreeDialog.showDialog(options);
    if (result != JOptionPane.CANCEL_OPTION) {
        GenerateTreeDialog.MethodTypes methodType = generateTreeDialog.getMethodType();
        PartitionData partition = generateTreeDialog.getDataPartition();
        Patterns patterns = new Patterns(partition.getAlignment());
        DistanceMatrix distances = new F84DistanceMatrix(patterns);
        Tree tree;
        TemporalRooting temporalRooting;
        switch(methodType) {
            case NJ:
                tree = new NeighborJoiningTree(distances);
                temporalRooting = new TemporalRooting(tree);
                tree = temporalRooting.findRoot(tree, TemporalRooting.RootingFunction.CORRELATION);
                break;
            case UPGMA:
                tree = new UPGMATree(distances);
                temporalRooting = new TemporalRooting(tree);
                break;
            default:
                throw new IllegalArgumentException("unknown method type");
        }
        tree.setId(generateTreeDialog.getName());
        options.userTrees.add(tree);
        treesTableModel.fireTableDataChanged();
        int row = options.userTrees.size() - 1;
        treesTable.getSelectionModel().setSelectionInterval(row, row);
    }
    fireTreePriorsChanged();
}

Example 8 with Patterns

use of dr.evolution.alignment.Patterns in project beast-mcmc by beast-dev.

the class BEAUTiImporter method importMicroSatFile.

// micro-sat
private void importMicroSatFile(File file) throws IOException, ImportException {
    try {
        Reader reader = new FileReader(file);
        BufferedReader bufferedReader = new BufferedReader(reader);
        MicroSatImporter importer = new MicroSatImporter(bufferedReader);
        List<Patterns> microsatPatList = importer.importPatterns();
        Taxa unionSetTaxonList = importer.getUnionSetTaxonList();
        Microsatellite microsatellite = importer.getMicrosatellite();
        //            options.allowDifferentTaxa = importer.isHasDifferentTaxon();
        bufferedReader.close();
        PartitionSubstitutionModel substModel = new PartitionSubstitutionModel(options, microsatPatList.get(0).getId());
        substModel.setMicrosatellite(microsatellite);
        for (Patterns patterns : microsatPatList) {
            setData(file.getName(), unionSetTaxonList, patterns, substModel, null);
        }
        // has to call after data is imported
        options.microsatelliteOptions.initModelParametersAndOpererators();
    } catch (ImportException e) {
        throw new ImportException(e.getMessage());
    } catch (IOException e) {
        throw new IOException(e.getMessage());
    }
}

Example 9 with Patterns

use of dr.evolution.alignment.Patterns in project beast-mcmc by beast-dev.

the class MsatFullLikelihoodTest method setUp.

public void setUp() throws Exception {
    super.setUp();
    //taxa
    ArrayList<Taxon> taxonList1 = new ArrayList<Taxon>();
    Collections.addAll(taxonList1, new Taxon("taxon1"), new Taxon("taxon2"), new Taxon("taxon3"));
    Taxa taxa1 = new Taxa(taxonList1);
    //msat datatype
    Microsatellite msat = new Microsatellite(1, 3);
    Patterns msatPatterns = new Patterns(msat, taxa1);
    //pattern in the correct code form.
    msatPatterns.addPattern(new int[] { 0, 1, 2 });
    //create tree
    NewickImporter importer = new NewickImporter("(taxon1:7.5,(taxon2:5.3,taxon3:5.3):2.2);");
    Tree tree = importer.importTree(null);
    //treeModel
    TreeModel treeModel = new TreeModel(tree);
    //msatsubstModel
    AsymmetricQuadraticModel aqm1 = new AsymmetricQuadraticModel(msat, null);
    //siteModel
    GammaSiteModel siteModel = new GammaSiteModel(aqm1);
    //treeLikelihood
    treeLikelihood1 = new TreeLikelihood(msatPatterns, treeModel, siteModel, null, null, false, false, true, false, false);
    setUpExample2();
    setUpExample3();
}

Example 10 with Patterns

use of dr.evolution.alignment.Patterns in project beast-mcmc by beast-dev.

the class MsatFullLikelihoodTest method setUpExample2.

private void setUpExample2() throws Exception {
    //taxa
    ArrayList<Taxon> taxonList2 = new ArrayList<Taxon>();
    Collections.addAll(taxonList2, new Taxon("taxon1"), new Taxon("taxon2"), new Taxon("taxon3"), new Taxon("taxon4"), new Taxon("taxon5"));
    Taxa taxa2 = new Taxa(taxonList2);
    //msat datatype
    Microsatellite msat = new Microsatellite(1, 3);
    Patterns msatPatterns = new Patterns(msat, taxa2);
    //pattern in the correct code form.
    msatPatterns.addPattern(new int[] { 0, 1, 2, 1, 2 });
    //create tree
    NewickImporter importer = new NewickImporter("(((taxon1:1.5,taxon2:1.5):1.5,(taxon3:2.1,taxon4:2.1):0.9):0.7,taxon5:3.7);");
    Tree tree = importer.importTree(null);
    //treeModel
    TreeModel treeModel = new TreeModel(tree);
    //msatsubstModel
    AsymmetricQuadraticModel aqm2 = new AsymmetricQuadraticModel(msat, null);
    //siteModel
    GammaSiteModel siteModel = new GammaSiteModel(aqm2);
    //treeLikelihood
    treeLikelihood2 = new TreeLikelihood(msatPatterns, treeModel, siteModel, null, null, false, false, true, false, false);
}