public Object parseXMLObject(XMLObject xo) throws XMLParseException {
final String fileName = xo.getStringAttribute(FILE_NAME);
// int burnin = 0;
// if (xo.hasAttribute(BURNIN)) {
// burnin = xo.getIntegerAttribute(BURNIN);
// }
Logger.getLogger("dr.evomodel")
.info("Creating the empirical tree distribution model, '" + xo.getId() + "'");
TaxonList taxa = (TaxonList) xo.getChild(TaxonList.class);
final File file = FileHelpers.getFile(fileName);
Tree[] trees = null;
try {
FileReader reader = new FileReader(file);
NexusImporter importer = new NexusImporter(reader);
trees = importer.importTrees(taxa);
} catch (FileNotFoundException e) {
throw new XMLParseException(e.getMessage());
} catch (IOException e) {
throw new XMLParseException(e.getMessage());
} catch (Importer.ImportException e) {
throw new XMLParseException(e.getMessage());
}
Logger.getLogger("dr.evomodel")
.info(" Read " + trees.length + " trees from file, " + fileName);
return new EmpiricalTreeDistributionModel(trees);
}
/**
* @param reader the readers to be analyzed
* @param burnin the burnin in states
* @param verbose true if progress should be logged to stdout
* @return an analyses of the trees in a log file.
* @throws java.io.IOException if general I/O error occurs
*/
public static ConditionalCladeFrequency analyzeLogFile(
Reader[] reader, double e, int burnin, boolean verbose) throws IOException {
TreeTrace[] trace = new TreeTrace[reader.length];
for (int i = 0; i < reader.length; i++) {
try {
trace[i] = TreeTrace.loadTreeTrace(reader[i]);
} catch (Importer.ImportException ie) {
throw new RuntimeException(ie.toString());
}
reader[i].close();
}
return new ConditionalCladeFrequency(trace, e, burnin, verbose);
}
protected boolean readFromFile(File file) throws IOException {
Reader reader = new FileReader(file);
BufferedReader bufferedReader = new BufferedReader(reader);
String line = bufferedReader.readLine();
while (line != null && line.length() == 0) {
line = bufferedReader.readLine();
}
boolean isNexus = (line != null && line.toUpperCase().contains("#NEXUS"));
reader = new FileReader(file);
Tree tree = null;
try {
if (isNexus) {
NexusImporter importer = new NexusImporter(reader);
tree = importer.importTree(taxa);
} else {
NewickImporter importer = new NewickImporter(reader);
tree = importer.importTree(taxa);
}
} catch (Importer.ImportException ime) {
JOptionPane.showMessageDialog(
this,
"Error parsing imported file: " + ime,
"Error reading file",
JOptionPane.ERROR_MESSAGE);
ime.printStackTrace();
return false;
} catch (IOException ioex) {
JOptionPane.showMessageDialog(
this, "File I/O Error: " + ioex, "File I/O Error", JOptionPane.ERROR_MESSAGE);
ioex.printStackTrace();
return false;
} catch (Exception ex) {
JOptionPane.showMessageDialog(
this, "Fatal exception: " + ex, "Error reading file", JOptionPane.ERROR_MESSAGE);
ex.printStackTrace();
return false;
}
if (tree == null) {
JOptionPane.showMessageDialog(
this,
"The file is not in a suitable format or contains no trees.",
"Error reading file",
JOptionPane.ERROR_MESSAGE);
return false;
}
FlexibleTree binaryTree = new FlexibleTree(tree, true);
binaryTree.resolveTree();
trees.add(binaryTree);
if (taxa == null) {
taxa = binaryTree;
}
getExportTreeAction().setEnabled(true);
getExportDataAction().setEnabled(true);
return true;
}