/*
* LoggerParser.java
*
* Copyright (c) 2002-2015 Alexei Drummond, Andrew Rambaut and Marc Suchard
*
* This file is part of BEAST.
* See the NOTICE file distributed with this work for additional
* information regarding copyright ownership and licensing.
*
* BEAST is free software; you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as
* published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
*
* BEAST is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public
* License along with BEAST; if not, write to the
* Free Software Foundation, Inc., 51 Franklin St, Fifth Floor,
* Boston, MA 02110-1301 USA
*/
package dr.inferencexml.loggers;
import dr.app.beast.BeastVersion;
import dr.inference.loggers.*;
import dr.math.MathUtils;
import dr.math.matrixAlgebra.SymmetricMatrix;
import dr.util.FileHelpers;
import dr.util.Identifiable;
import dr.util.Property;
import dr.xml.*;
import java.io.File;
import java.io.PrintWriter;
import java.util.Date;
/**
* @author Alexei Drummond
* @author Andrew Rambaut
*/
public class LoggerParser extends AbstractXMLObjectParser {
public static final String LOG = "log";
public static final String ECHO = "echo";
public static final String ECHO_EVERY = "echoEvery";
public static final String TITLE = "title";
public static final String HEADER = "header";
public static final String FILE_NAME = FileHelpers.FILE_NAME;
public static final String FORMAT = "format";
public static final String TAB = "tab";
public static final String HTML = "html";
public static final String PRETTY = "pretty";
public static final String LOG_EVERY = "logEvery";
public static final String ALLOW_OVERWRITE_LOG = "overwrite";
public static final String COLUMNS = "columns";
public static final String COLUMN = "column";
public static final String LABEL = "label";
public static final String SIGNIFICANT_FIGURES = "sf";
public static final String DECIMAL_PLACES = "dp";
public static final String WIDTH = "width";
public String getParserName() {
return LOG;
}
/**
* @return an object based on the XML element it was passed.
*/
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
// You must say how often you want to log
final int logEvery = xo.getIntegerAttribute(LOG_EVERY);
final PrintWriter pw = getLogFile(xo, getParserName());
final LogFormatter formatter = new TabDelimitedFormatter(pw);
boolean performanceReport = false;
if (!xo.hasAttribute(FILE_NAME)) {
// is a screen log
performanceReport = true;
}
// added a performance measurement delay to avoid the full evaluation period.
final MCLogger logger = new MCLogger(formatter, logEvery, performanceReport, 10000);
String title = null;
if (xo.hasAttribute(TITLE)) {
title = xo.getStringAttribute(TITLE);
}
String header = null;
if (xo.hasAttribute(HEADER)) {
header = xo.getStringAttribute(HEADER);
}
if (title == null) {
final BeastVersion version = new BeastVersion();
title = "BEAST " + version.getVersionString() + "\n" +
(header != null ? header + "\n" : "") +
"Generated " + (new Date()).toString() + " [seed=" + MathUtils.getSeed() + "]\n" +
System.getProperty("command_line", "");
} else {
if (header != null) {
title += "\n" + header;
}
}
logger.setTitle(title);
for (int i = 0; i < xo.getChildCount(); i++) {
final 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 if (child instanceof Property) {
logger.addColumn(new LogColumn.Default(((Property) child).getAttributeName(), child));
} else {
logger.addColumn(new LogColumn.Default(child.getClass().toString(), child));
}
}
return logger;
}
public static PrintWriter getLogFile(XMLObject xo, String parserName) throws XMLParseException {
return XMLParser.getFilePrintWriter(xo, parserName);
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private final XMLSyntaxRule[] rules = {
AttributeRule.newIntegerRule(LOG_EVERY),
AttributeRule.newBooleanRule(ALLOW_OVERWRITE_LOG, true),
new StringAttributeRule(FILE_NAME,
"The name of the file to send log output to. " +
"If no file name is specified then log is sent to standard output", true),
new StringAttributeRule(TITLE,
"The title of the log", true),
new StringAttributeRule(HEADER,
"The subtitle of the log", true),
new OrRule(
new XMLSyntaxRule[]{
new ElementRule(Columns.class, 1, Integer.MAX_VALUE),
new ElementRule(Loggable.class, 1, Integer.MAX_VALUE),
new ElementRule(Object.class, 1, Integer.MAX_VALUE)
}
)
};
public String getParserDescription() {
return "Logs one or more items at a given frequency to the screen or to a file";
}
public Class getReturnType() {
return MLLogger.class;
}
}