/*
* MixtureModelLogAnalyser.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.app.tools;
import dr.app.beast.BeastVersion;
import dr.app.util.Arguments;
import dr.app.util.Utils;
import dr.inference.trace.PathSamplingAnalysis;
import dr.inference.trace.TraceException;
import dr.util.Attribute;
import dr.util.FileHelpers;
import dr.util.Version;
import dr.xml.AbstractXMLObjectParser;
import dr.xml.AttributeRule;
import dr.xml.ElementRule;
import dr.xml.StringAttributeRule;
import dr.xml.XMLObject;
import dr.xml.XMLObjectParser;
import dr.xml.XMLParseException;
import dr.xml.XMLSyntaxRule;
import java.io.*;
import java.util.*;
/**
* @author Wai Lok Sibon Li
*/
public class MixtureModelLogAnalyser {
private final static Version version = new BeastVersion();
public static final String MIXTURE_MODEL_LOG_ANALYSER = "mixtureModelLogAnalyser";
public static final String BURNIN = "burnin";
public static final String DISCRETE_VARIABLE = "discreteVariable";
public MixtureModelLogAnalyser(int burnin, String inputFileName, String outputFileName, String discreteVariableName
) throws IOException, TraceException {
File parentFile = new File(inputFileName);
if (parentFile.isDirectory()) {
System.out.println("Analysing all log files below directory: " + inputFileName);
} else if (parentFile.isFile()) {
System.out.println("Analysing log file: " + inputFileName);
} else {
System.err.println(inputFileName + " does not exist!");
System.exit(0);
}
if (outputFileName != null) {
FileOutputStream outputStream = new FileOutputStream(outputFileName);
System.setOut(new PrintStream(outputStream));
}
analyze(parentFile, burnin, discreteVariableName);
}
/**
* Recursively analyzes log files.
*
* @param file the file to analyze (if this is a directory then the files within it are analyzed)
* @param burnin the burnin to use
* @param discreteVariableName tag for the name of the discrete variable
* @throws dr.inference.trace.TraceException
* if the trace file is in the wrong format or corrupted
*/
private void analyze(File file, int burnin, String discreteVariableName) throws TraceException {
if (file.isFile()) {
try {
String name = file.getCanonicalPath();
report(name, burnin, discreteVariableName);
} catch (IOException e) {
//e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
}
} else {
File[] files = file.listFiles();
for (File f : files) {
if (f.isDirectory()) {
analyze(f, burnin, discreteVariableName);
} else if (f.getName().endsWith(".log")) {
analyze(f, burnin, discreteVariableName);
}
}
}
}
/**
* Recursively analyzes trees files.
*
* @param name the file to analyze (if this is a directory then the files within it are analyzed)
* @param burnin the burnin to use
* @param discreteVariableName tag for the name of the discrete variable
*/
private void report(String name, int burnin, String discreteVariableName) {
try {
FileReader fileReader = new FileReader(new File(name));
BufferedReader br = new BufferedReader(fileReader);
String line;
String previousLine =null;
int discreteVariableIndex = -1;
Hashtable<String, Integer> hash = new Hashtable<String, Integer>();
while((line=br.readLine()) != null) {
if(line.matches("\\d+\\t.+")) {
String[] split = line.split("\t");
if(split[0].equals("0")) {
String[] headerSplit = previousLine.split("\t");
for(int i=0; i<headerSplit.length; i++) {
String s = headerSplit[i];
if(s.equals(discreteVariableName)) {
discreteVariableIndex = i;
}
}
}
if(Integer.parseInt(split[0])>=burnin) {
if(hash.containsKey(split[discreteVariableIndex])) {
hash.put(split[discreteVariableIndex], new Integer(hash.get(split[discreteVariableIndex]) + 1));
}
else {
hash.put(split[discreteVariableIndex], new Integer(1));
}
}
}
previousLine = line;
}
Vector<String> v = new Vector(hash.keySet());
Collections.sort(v);
System.out.print("name" + "\t");
for(String s : v) {
double state = Double.parseDouble(s);
if(Math.floor(state)!=state) {
throw new RuntimeException("State is not a whole number: " + state);
}
System.out.print("state " + (int) state + "\t");
}
System.out.print("\n" + name + "\t");
for (String aV : v) {
String element = aV;
System.out.print(hash.get(element) + "\t");
}
System.out.println();
br.close();
} catch (IOException e) {
System.err.println("Error Parsing Input log: " + e.getMessage());
}
}
public static XMLObjectParser PARSER = new AbstractXMLObjectParser() {
public String getParserName() {
return MIXTURE_MODEL_LOG_ANALYSER;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
try {
String inputFileName = xo.getStringAttribute(FileHelpers.FILE_NAME);
String discreteVariableName = xo.getStringAttribute(DISCRETE_VARIABLE);
int burninLength = 0;
if (xo.hasAttribute(BURNIN)) {
burninLength = xo.getIntegerAttribute(BURNIN);
}
MixtureModelLogAnalyser mixtureModel = new MixtureModelLogAnalyser(burninLength, inputFileName, null, discreteVariableName);
return mixtureModel;
} catch (IOException ioe) {
throw new XMLParseException(ioe.getMessage());
} catch (TraceException te) {
throw new XMLParseException(te.getMessage());
}
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public String getParserDescription() {
return "Performs posterior probabilities calculations.";
}
public Class getReturnType() {
return MixtureModelLogAnalyser.class;
}
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private final XMLSyntaxRule[] rules = {
new StringAttributeRule(FileHelpers.FILE_NAME,
"The traceName of a BEAST log file (can not include trees, which should be logged separately"),
new StringAttributeRule(DISCRETE_VARIABLE,
"The tag name of the discrete variable"),
AttributeRule.newIntegerRule(BURNIN, true),
};
};
public static void printTitle() {
System.out.println();
centreLine("MixtureModelLogAnalyser " + version.getVersionString() + ", " + version.getDateString(), 60);
centreLine("MCMC Output analysis", 60);
centreLine("by", 60);
centreLine("Andrew Rambaut and Alexei J. Drummond", 60);
System.out.println();
centreLine("Institute of Evolutionary Biology", 60);
centreLine("University of Edinburgh", 60);
centreLine("a.rambaut@ed.ac.uk", 60);
System.out.println();
centreLine("Department of Computer Science", 60);
centreLine("University of Auckland", 60);
centreLine("alexei@cs.auckland.ac.nz", 60);
System.out.println();
System.out.println();
}
public static void centreLine(String line, int pageWidth) {
int n = pageWidth - line.length();
int n1 = n / 2;
for (int i = 0; i < n1; i++) {
System.out.print(" ");
}
System.out.println(line);
}
public static void printUsage(Arguments arguments) {
arguments.printUsage("mixturemodelloganalyser", "[-burnin <burnin>][<input-file-name> [<output-file-name>]]");
System.out.println();
System.out.println(" Example: treelengthfinder test.log");
System.out.println(" Example: treelengthfinder -burnin 10000 -discreteVariable branchRates.distributionIndex trees.log out.txt");
System.out.println();
}
//Main method
public static void main(String[] args) throws IOException, TraceException {
printTitle();
Arguments arguments = new Arguments(
new Arguments.Option[]{
new Arguments.IntegerOption("burnin", "the number of states to be considered as 'burn-in'"),
new Arguments.StringOption("discreteVariable", "variable_name", "indicates the name of a variable that is actually discrete in nature"),
new Arguments.Option("help", "option to print this message")
});
try {
arguments.parseArguments(args);
} catch (Arguments.ArgumentException ae) {
System.out.println(ae);
printUsage(arguments);
System.exit(1);
}
if (arguments.hasOption("help")) {
printUsage(arguments);
System.exit(0);
}
int burnin = -1;
if (arguments.hasOption("burnin")) {
burnin = arguments.getIntegerOption("burnin");
}
String discreteVariableName = null;
if (arguments.hasOption("discreteVariable")) {
discreteVariableName = arguments.getStringOption("discreteVariable");
}
String inputFileName = null;
String outputFileName = null;
String[] args2 = arguments.getLeftoverArguments();
if (args2.length > 2) {
System.err.println("Unknown option: " + args2[2]);
System.err.println();
printUsage(arguments);
System.exit(1);
}
if (args2.length > 0) {
inputFileName = args2[0];
}
if (args2.length > 1) {
outputFileName = args2[1];
}
if (inputFileName == null) {
// No input file name was given so throw up a dialog box...
inputFileName = Utils.getLoadFileName("MixtureModelLogAnalyser " + version.getVersionString() + " - Select log file to analyse");
}
if(burnin==-1) {
System.out.println("Enter number of trees to burn-in (integer): ");
BufferedReader br = new BufferedReader(new InputStreamReader(System.in));
burnin = Integer.parseInt(br.readLine());
}
if(discreteVariableName==null) {
System.out.println("Enter name of discrete variable: ");
BufferedReader br = new BufferedReader(new InputStreamReader(System.in));
discreteVariableName = br.readLine();
}
new MixtureModelLogAnalyser(burnin, inputFileName, outputFileName, discreteVariableName/*, !shortReport, hpds, ess, stdErr, marginalLikelihood*/);
System.exit(0);
}
}