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

Example 26 with Taxa

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

the class TaxonSetPanel method setCurrentTaxonSet.

protected void setCurrentTaxonSet(Taxa taxonSet) {
    this.currentTaxonSet = taxonSet;
    includedTaxa.clear();
    excludedTaxa.clear();
    if (currentTaxonSet != null) {
        for (int i = 0; i < taxonSet.getTaxonCount(); i++) {
            includedTaxa.add(taxonSet.getTaxon(i));
        }
        Collections.sort(includedTaxa);
        // get taxa associated to each tree
        PartitionTreeModel treeModel = options.taxonSetsTreeModel.get(currentTaxonSet);
        TaxonList alignment = options.getDataPartitions(treeModel).get(0).getTaxonList();
        Taxa taxa = new Taxa(alignment);
        for (int i = 0; i < taxa.getTaxonCount(); i++) {
            excludedTaxa.add(taxa.getTaxon(i));
        }
        excludedTaxa.removeAll(includedTaxa);
        Collections.sort(excludedTaxa);
    }
    setTaxonSetTitle();
    setupTaxonSetsComboBoxes();
    includedTaxaTableModel.fireTableDataChanged();
    excludedTaxaTableModel.fireTableDataChanged();
}

Example 27 with Taxa

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

the class TaxonSetPanel method importTaxonSets.

public void importTaxonSets() {
    File[] files = frame.selectImportFiles("Import Taxon Set File...", false, new FileNameExtensionFilter[] { new FileNameExtensionFilter("Tab-delimited text files", "txt", "tab", "dat") });
    DataTable<String[]> dataTable;
    if (files != null && files.length != 0) {
        try {
            // Load the file as a table
            dataTable = DataTable.Text.parse(new FileReader(files[0]), false, true, false, false);
        } catch (FileNotFoundException fnfe) {
            JOptionPane.showMessageDialog(this, "Unable to open file: File not found", "Unable to open file", JOptionPane.ERROR_MESSAGE);
            return;
        } catch (IOException ioe) {
            JOptionPane.showMessageDialog(this, "Unable to read file: " + ioe.getMessage(), "Unable to read file", JOptionPane.ERROR_MESSAGE);
            return;
        } catch (Exception ex) {
            ex.printStackTrace(System.err);
            JOptionPane.showMessageDialog(this, "Fatal exception: " + ex, "Error reading file", JOptionPane.ERROR_MESSAGE);
            ex.printStackTrace();
            return;
        }
    } else {
        return;
    }
    String[] taxonNames = dataTable.getRowLabels();
    if (dataTable.getColumnCount() == 0) {
        String name = files[0].getName();
        int lastDot = name.lastIndexOf('.');
        if (lastDot >= 1) {
            name = name.substring(0, lastDot);
        }
        Taxa taxa = new Taxa();
        // Only one column so assume the entire set is defined in this file.
        for (String taxonName : taxonNames) {
            final int index = options.taxonList.getTaxonIndex(taxonName);
            if (index >= 0) {
                taxa.addTaxon(options.taxonList.getTaxon(index));
            }
        }
        taxa.setId(name);
        options.taxonSets.add(taxa);
        options.taxonSetsTreeModel.put(taxa, options.getPartitionTreeModels().get(0));
    } else {
        // assume column one is the taxon labels and column two is the set names
        String[] taxonSetNames = dataTable.getColumn(0);
        Map<String, Taxa> taxonSets = new HashMap<String, Taxa>();
        int i = 0;
        for (String taxonName : taxonNames) {
            final int index = options.taxonList.getTaxonIndex(taxonName);
            if (index >= 0) {
                Taxa taxa = taxonSets.get(taxonSetNames[i]);
                if (taxa == null) {
                    taxa = new Taxa();
                    taxa.setId(taxonSetNames[i]);
                    taxonSets.put(taxonSetNames[i], taxa);
                }
                taxa.addTaxon(options.taxonList.getTaxon(index));
            }
            i++;
        }
        for (Taxa taxa : taxonSets.values()) {
            options.taxonSets.add(taxa);
            options.taxonSetsTreeModel.put(taxa, options.getPartitionTreeModels().get(0));
            options.taxonSetsMono.put(taxa, false);
            options.taxonSetsIncludeStem.put(taxa, false);
            options.taxonSetsHeights.put(taxa, 0.0);
        }
    }
    taxonSetsTableModel.fireTableDataChanged();
}

Example 28 with Taxa

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

the class BEAUTiImporter method addTaxonSets.

private void addTaxonSets(TaxonList taxonList, List<NexusApplicationImporter.TaxSet> taxSets) throws ImportException {
    if (taxSets != null) {
        for (NexusApplicationImporter.TaxSet taxSet : taxSets) {
            Taxa taxa = new Taxa(taxSet.getName());
            for (CharSetBlock block : taxSet.getBlocks()) {
                for (int i = block.getFromSite(); i <= block.getToSite(); i++) {
                    taxa.addTaxon(taxonList.getTaxon(i - 1));
                }
            }
            options.taxonSets.add(taxa);
            options.taxonSetsTreeModel.put(taxa, options.getPartitionTreeModels().get(0));
            options.taxonSetsMono.put(taxa, false);
            options.taxonSetsIncludeStem.put(taxa, false);
            options.taxonSetsHeights.put(taxa, 0.0);
        }
    }
}

Example 29 with Taxa

use of dr.evolution.util.Taxa 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 30 with Taxa

use of dr.evolution.util.Taxa 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, null, importedTraits, null);
}