/*
* ARGLogger.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.evomodel.arg;
import dr.evoxml.util.GraphMLUtils;
import dr.inference.loggers.LogFormatter;
import dr.inference.loggers.MCLogger;
import dr.inference.loggers.MLLogger;
import dr.inference.loggers.TabDelimitedFormatter;
import dr.xml.*;
import org.jdom.Element;
import org.jdom.output.XMLOutputter;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.PrintWriter;
import java.util.logging.Logger;
/**
* Created by IntelliJ IDEA.
* User: msuchard
* Date: Jan 13, 2007
* Time: 2:16:08 PM
* To change this template use File | Settings | File Templates.
*/
public class ARGLogger extends MCLogger {
public static final String LOG_ARG = "logArg";
public static final String DOT_FORMAT = "dotFormat";
public static final String COMPRESSED_STRING = "compressedString";
public static final String EXTENDED_NEWICK = "extendedNewick";
public static final String STRIPPED_NEWICK = "strippedNewick";
public static final String FULL_STRING = "fullString";
public static final String DISTINCT_TREES = "distinctTrees";
public static final String FORMAT = "format";
// The following were in MCLogger; where did they go?
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 FILE_NAME = "fileName";
// 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 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";
private ARGModel argModel;
private String formatType;
private ARGDistinctTreeCountStatistic treeStat;
public ARGLogger(ARGModel argModel, LogFormatter formatter, int logEvery, String formatType) {
super(formatter, logEvery, false);
this.argModel = argModel;
this.formatType = formatType;
if(formatType.equals(DISTINCT_TREES)){
treeStat = new ARGDistinctTreeCountStatistic(argModel);
}
}
public static final String GRAPHML_HEADER = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<graphml xmlns=\"http://graphml.graphdrawing.org/xmlns\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:schemaLocation=\"http://graphml.graphdrawing.org/xmlns http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd\">";
public static final String GRAPHML_FOOTER = "</graphml>";
public void startLogging() {
if (formatType.equals(EXTENDED_NEWICK)) {
logLine("stateARG.string");
} else if (formatType.equals(STRIPPED_NEWICK)) {
logLine("StrippedARGString");
} else {
logLine(GRAPHML_HEADER);
}
// if (!dotFormat && !newickFormat)
// logLine(GRAPHML_HEADER);
// if (newickFormat)
// logLine("state ARG.string");
}
public void stopLogging() {
if (!formatType.equals(EXTENDED_NEWICK) && !formatType.equals(STRIPPED_NEWICK)) {
logLine(GRAPHML_FOOTER);
}
// if (!dotFormat && !newickFormat)
// logLine(GRAPHML_FOOTER);
}
static XMLOutputter outputter = new XMLOutputter(org.jdom.output.Format.getPrettyFormat());
public void log(long state) {
if (logEvery <= 0 || ((state % logEvery) == 0)) {
Element graphElement = argModel.toXML();
graphElement.setAttribute(ARGModel.ID_ATTRIBUTE, "STATE_" + state);
if (formatType.equals(DOT_FORMAT))
logLine(GraphMLUtils.dotFormat(graphElement));
else if (formatType.equals(COMPRESSED_STRING))
logLine("ARG STATE_" + state + " = " + argModel.toGraphStringCompressed(false));
else if (formatType.equals(FULL_STRING))
logLine(outputter.outputString(graphElement));
else if (formatType.equals(EXTENDED_NEWICK))
logLine(argModel.toExtendedNewick());
else if (formatType.equals(DISTINCT_TREES))
logLine(treeStat.getStatisticValue(0) + "\t" + treeStat.getFullOutput());
else
logLine(argModel.toStrippedNewick());
}
// logLine("ARG STATE_" + state + " = " + argModel.toExtendedNewick());
}
public static XMLObjectParser PARSER = new AbstractXMLObjectParser() {
public String getParserName() {
return LOG_ARG;
}
/**
* @return an object based on the XML element it was passed.
*/
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
ARGModel argModel = (ARGModel) xo.getChild(ARGModel.class);
String fileName = null;
String title = null;
String argModelLoggerFormat = null;
// boolean dotFormat = false;
// boolean newickFormat = false;
// boolean nexusFormat = false;
//
// String colouringLabel = "demes";
// String rateLabel = "rate";
// String likelihoodLabel = "lnP";
if (xo.hasAttribute(TITLE)) {
title = xo.getStringAttribute(TITLE);
}
if (xo.hasAttribute(FILE_NAME)) {
fileName = xo.getStringAttribute(FILE_NAME);
}
if (xo.hasAttribute(FORMAT)) {
argModelLoggerFormat = xo.getStringAttribute(FORMAT);
}
// boolean substitutions = false;
// if (xo.hasAttribute(BRANCH_LENGTHS)) {
// substitutions = xo.getStringAttribute(BRANCH_LENGTHS).equals(SUBSTITUTIONS);
// }
// BranchRateModel branchRateModel = (BranchRateModel) xo.getChild(BranchRateModel.class);
// ColourSamplerModel colourSamplerModel = (ColourSamplerModel) xo.getChild(ColourSamplerModel.class);
// Likelihood likelihood = (Likelihood) xo.getChild(Likelihood.class);
// logEvery of zero only displays at the end
int logEvery = 1;
if (xo.hasAttribute(LOG_EVERY)) {
logEvery = xo.getIntegerAttribute(LOG_EVERY);
}
PrintWriter pw;
if (fileName != null) {
try {
File file = new File(fileName);
String name = file.getName();
String parent = file.getParent();
if (!file.isAbsolute()) {
parent = System.getProperty("user.dir");
}
// System.out.println("Writing log file to "+parent+System.getProperty("path.separator")+name);
pw = new PrintWriter(new FileOutputStream(new File(parent, name)));
} catch (FileNotFoundException fnfe) {
throw new XMLParseException("File '" + fileName + "' can not be opened for " + getParserName() + " element.");
}
} else {
pw = new PrintWriter(System.out);
}
LogFormatter formatter = new TabDelimitedFormatter(pw);
Logger.getLogger("dr.evomodel").info("Creating " + LOG_ARG + " of type " + argModelLoggerFormat);
ARGLogger logger = new ARGLogger(argModel, formatter, logEvery, argModelLoggerFormat);
// TreeLogger logger = new TreeLogger(tree, branchRateModel, rateLabel,
// colourSamplerModel, colouringLabel, likelihood, likelihoodLabel,
// formatter, logEvery, nexusFormat, substitutions);
if (title != null) {
logger.setTitle(title);
}
return logger;
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
String[] validFormats = {DOT_FORMAT, EXTENDED_NEWICK,
COMPRESSED_STRING, FULL_STRING, STRIPPED_NEWICK, DISTINCT_TREES};
private XMLSyntaxRule[] rules = new XMLSyntaxRule[]{
AttributeRule.newIntegerRule(LOG_EVERY),
new StringAttributeRule(FORMAT, "The type logger's output type",
validFormats, false),
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),
// AttributeRule.newBooleanRule(NEXUS_FORMAT, true,
// "Whether to use the NEXUS format for the tree log"),
// new StringAttributeRule(BRANCH_LENGTHS, "What units should the branch lengths be in", new String[]{TIME, SUBSTITUTIONS}, true),
new ElementRule(ARGModel.class, "The ARG which is to be logged"),
// new ElementRule(BranchRateModel.class, true),
// new ElementRule(ColourSamplerModel.class, true),
// new ElementRule(Likelihood.class, true)
};
public String getParserDescription() {
return "Logs an ARG to a file";
}
public String getExample() {
return
"<!-- The " + getParserName() + " element takes an argModel to be logged -->\n" +
"<" + getParserName() + " " + LOG_EVERY + "=\"100\" " + FILE_NAME + "=\"log.args\">\n" +
" <argModel idref=\"treeModel1\"/>\n" +
"</" + getParserName() + ">\n";
}
public Class getReturnType() {
return MLLogger.class;
}
};
}