use of dr.evolution.io.NewickImporter in project beast-mcmc by beast-dev.
the class CompleteHistorySimulatorTest method setUp.
public void setUp() throws Exception {
super.setUp();
MathUtils.setSeed(666);
NewickImporter importer = new NewickImporter("(1:2.0,(2:1.0,3:1.0):1.0);");
tree = importer.importTree(null);
treeModel = new TreeModel("treeModel", tree);
}
use of dr.evolution.io.NewickImporter in project beast-mcmc by beast-dev.
the class BetaTreeDiversityStatistic method main.
public static void main(String[] arg) throws IOException, Importer.ImportException {
Tree tree = (new NewickImporter("((A:1,B:1):1,(C:1, D:1):1);")).importNextTree();
BetaTreeDiversityStatistic statistic = (BetaTreeDiversityStatistic) BetaTreeDiversityStatistic.FACTORY.createStatistic();
Taxa taxa = new Taxa();
taxa.addTaxon(new Taxon("A"));
taxa.addTaxon(new Taxon("C"));
statistic.setTaxonList(taxa);
System.out.println(statistic.getSummaryStatistic(tree)[0]);
}
use of dr.evolution.io.NewickImporter in project beast-mcmc by beast-dev.
the class BirthDeathSerialSkylineModel method main.
public static void main(String[] args) throws IOException, Importer.ImportException {
// test framework
Variable<Double> times = new Variable.D(1, 10);
Variable<Double> mu = new Variable.D(1, 10);
for (int i = 0; i < mu.getSize(); i++) {
times.setValue(i, (i + 1) * 2.0);
mu.setValue(i, i + 1.0);
}
Variable<Double> lambda = new Variable.D(1, 10);
Variable<Double> psi = new Variable.D(0.5, 1);
Variable<Double> p = new Variable.D(0.5, 1);
Variable<Double> origin = new Variable.D(0.5, 1);
boolean relativeDeath = false;
boolean sampledIndividualsRemainInfectious = false;
boolean timesStartFromOrigin = false;
BirthDeathSerialSkylineModel model = new BirthDeathSerialSkylineModel(times, lambda, mu, psi, p, origin, relativeDeath, sampledIndividualsRemainInfectious, timesStartFromOrigin, Type.SUBSTITUTIONS);
NewickImporter importer = new NewickImporter("((A:6,B:5):4,(C:3,D:2):1);");
Tree tree = importer.importNextTree();
model.calculateTreeLogLikelihood(tree);
for (int i = 0; i < times.getSize(); i += 1) {
System.out.println("mu at time " + i + " is " + model.mu(i));
System.out.println("p0 at time " + i + " is " + model.p0(0, i, i));
}
}
use of dr.evolution.io.NewickImporter in project beast-mcmc by beast-dev.
the class NewickParser method parseXMLObject.
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
final Units.Type units = XMLUnits.Utils.getUnitsAttr(xo);
// boolean usingDates = xo.getAttribute(USING_DATES, true);
boolean usingDates = true;
if (xo.hasAttribute(USING_DATES)) {
usingDates = xo.getAttribute(USING_DATES, true);
}
boolean usingHeights = false;
if (xo.hasAttribute(USING_HEIGHTS)) {
usingHeights = xo.getAttribute(USING_HEIGHTS, true);
}
if (usingDates && usingHeights) {
throw new XMLParseException("Unable to use both dates and node heights. Specify value of usingDates attribute.");
}
// else if (!usingDates && !usingHeights) {
// System.out.println("Tree is assumed to be ultrametric");
// }
StringBuffer buffer = new StringBuffer();
for (int i = 0; i < xo.getChildCount(); i++) {
if (xo.getChild(i) instanceof String) {
buffer.append((String) xo.getChild(i));
} else {
throw new XMLParseException("illegal element in newick element");
}
}
java.io.Reader reader = new java.io.StringReader(buffer.toString());
NewickImporter importer = new NewickImporter(reader);
FlexibleTree tree;
try {
tree = (FlexibleTree) importer.importTree(null);
} catch (IOException ioe) {
throw new XMLParseException("error parsing tree in newick element");
} catch (NewickImporter.BranchMissingException bme) {
throw new XMLParseException("branch missing in tree in newick element");
} catch (Importer.ImportException ime) {
throw new XMLParseException("error parsing tree in newick element - " + ime.getMessage());
}
if (tree == null) {
throw new XMLParseException("Failed to read tree");
}
tree.setUnits(units);
for (int i = 0; i < tree.getTaxonCount(); i++) {
FlexibleNode node = (FlexibleNode) tree.getExternalNode(i);
String id = node.getTaxon().getId();
Taxon taxon = null;
XMLObject obj = getStore().get(id);
if (obj != null && obj.getNativeObject() instanceof Taxon) {
taxon = (Taxon) obj.getNativeObject();
}
if (taxon != null) {
node.setTaxon(taxon);
} else {
throw new XMLParseException("unknown taxon, " + id + ", in newick tree");
}
}
if (usingDates) {
for (int i = 0; i < tree.getTaxonCount(); i++) {
NodeRef node = tree.getExternalNode(i);
dr.evolution.util.Date date = (dr.evolution.util.Date) tree.getTaxonAttribute(i, dr.evolution.util.Date.DATE);
if (date == null) {
date = (dr.evolution.util.Date) tree.getNodeAttribute(tree.getExternalNode(i), dr.evolution.util.Date.DATE);
}
double height = 0.0;
double nodeHeight = tree.getNodeHeight(node);
if (date != null) {
height = Taxon.getHeightFromDate(date);
}
if (Math.abs(nodeHeight - height) > 1e-5) {
System.out.println(" Changing height of node " + tree.getTaxon(node.getNumber()) + " from " + nodeHeight + " to " + height);
tree.setNodeHeight(node, height);
}
}
for (int i = 0; i < tree.getInternalNodeCount(); i++) {
dr.evolution.util.Date date = (dr.evolution.util.Date) tree.getNodeAttribute(tree.getInternalNode(i), dr.evolution.util.Date.DATE);
if (date != null) {
double height = Taxon.getHeightFromDate(date);
tree.setNodeHeight(tree.getInternalNode(i), height);
}
}
// END: i loop
MutableTree.Utils.correctHeightsForTips(tree);
} else if (!usingDates && !usingHeights) {
System.out.println("Tree is assumed to be ultrametric");
// not using dates or heights
for (int i = 0; i < tree.getTaxonCount(); i++) {
final NodeRef leaf = tree.getExternalNode(i);
final double h = tree.getNodeHeight(leaf);
if (h != 0.0) {
double zero = 0.0;
System.out.println(" Changing height of leaf node " + tree.getTaxon(leaf.getNumber()) + " from " + h + " to " + zero);
tree.setNodeHeight(leaf, zero);
}
}
// END: i loop
} else {
System.out.println("Using node heights.");
}
if (xo.hasAttribute(RESCALE_HEIGHT)) {
double rescaleHeight = xo.getDoubleAttribute(RESCALE_HEIGHT);
double scale = rescaleHeight / tree.getNodeHeight(tree.getRoot());
for (int i = 0; i < tree.getInternalNodeCount(); i++) {
NodeRef n = tree.getInternalNode(i);
tree.setNodeHeight(n, tree.getNodeHeight(n) * scale);
}
}
if (xo.hasAttribute(RESCALE_LENGTH)) {
double rescaleLength = xo.getDoubleAttribute(RESCALE_LENGTH);
double scale = rescaleLength / TreeUtils.getTreeLength(tree, tree.getRoot());
for (int i = 0; i < tree.getInternalNodeCount(); i++) {
NodeRef n = tree.getInternalNode(i);
tree.setNodeHeight(n, tree.getNodeHeight(n) * scale);
}
}
//System.out.println("Constructed newick tree = " + Tree.Utils.uniqueNewick(tree, tree.getRoot()));
return tree;
}
use of dr.evolution.io.NewickImporter in project beast-mcmc by beast-dev.
the class DataModelImporter method importFromTreeFile.
public Map importFromTreeFile(String fileName, Map dataModel) throws IOException, Importer.ImportException {
Tree tree = null;
try {
Reader reader = new FileReader(fileName);
BufferedReader bufferedReader = new BufferedReader(reader);
String line = bufferedReader.readLine();
while (line != null && line.length() == 0) {
line = bufferedReader.readLine();
}
reader = new FileReader(fileName);
if ((line != null && line.toUpperCase().contains("#NEXUS"))) {
// is a NEXUS file
NexusImporter importer = new NexusImporter(reader);
tree = importer.importNextTree();
} else {
NewickImporter importer = new NewickImporter(reader);
tree = importer.importNextTree();
}
bufferedReader.close();
} catch (IOException e) {
throw new IOException(e.getMessage());
}
if (tree != null) {
dataModel.put("tree", TreeUtils.newick(tree));
}
return dataModel;
}
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