package dr.inferencexml.loggers; import dr.inference.loggers.*; import dr.inference.model.Likelihood; import dr.util.Identifiable; import dr.xml.*; import java.io.PrintWriter; /** * */ public class MLLoggerParser extends LoggerParser { public static final String LOG_ML = "logML"; public static final String LIKELIHOOD = "ml"; public String getParserName() { return LOG_ML; } public Object parseXMLObject(XMLObject xo) throws XMLParseException { Likelihood likelihood = (Likelihood) xo.getElementFirstChild(LIKELIHOOD); // logEvery of zero only displays at the end int logEvery = xo.getAttribute(LOG_EVERY, 0); final PrintWriter pw = getLogFile(xo, getParserName()); LogFormatter formatter = new TabDelimitedFormatter(pw); MLLogger logger = new MLLogger(likelihood, formatter, logEvery); if (xo.hasAttribute(TITLE)) { logger.setTitle(xo.getStringAttribute(TITLE)); } for (int i = 0; i < xo.getChildCount(); i++) { Object child = xo.getChild(i); if (child instanceof Columns) { logger.addColumns(((Columns) child).getColumns()); } else if (child instanceof Loggable) { logger.add((Loggable) child); } else if (child instanceof Identifiable) { logger.addColumn(new LogColumn.Default(((Identifiable) child).getId(), child)); } else { logger.addColumn(new LogColumn.Default(child.getClass().toString(), child)); } } return logger; } //************************************************************************ // AbstractXMLObjectParser implementation //************************************************************************ public XMLSyntaxRule[] getSyntaxRules() { return rules; } private final XMLSyntaxRule[] rules = { AttributeRule.newIntegerRule(LOG_EVERY, true), new ElementRule(LIKELIHOOD, new XMLSyntaxRule[]{new ElementRule(Likelihood.class)}), new OrRule( new ElementRule(Columns.class, 1, Integer.MAX_VALUE), new ElementRule(Loggable.class, 1, Integer.MAX_VALUE) ) }; public String getParserDescription() { return "Logs one or more items every time the given likelihood improves"; } public Class getReturnType() { return MLLogger.class; } }