/*
* NodeStateAnalyser.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.util.Version;
import dr.evolution.io.TreeImporter;
import dr.evolution.io.NexusImporter;
import dr.evolution.io.Importer;
import dr.evolution.tree.Tree;
import dr.evolution.tree.NodeRef;
import java.io.*;
import java.util.*;
public class NodeStateAnalyser {
private final static Version version = new BeastVersion();
public NodeStateAnalyser(int burnin, double mrsd, double scale, String inputFileName, String outputFileName) throws IOException {
File parentFile = new File(inputFileName);
if (parentFile.isDirectory()) {
System.out.println("Analysing all trees files below directory: " + inputFileName);
} else if (parentFile.isFile()) {
System.out.println("Analysing tree 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, mrsd, scale);
}
/**
* 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
* @throws dr.inference.trace.TraceException
* if the trace file is in the wrong format or corrupted
*/
private void analyze(File file, int burnin, double mrsd, double scale) {
if (file.isFile()) {
try {
String name = file.getCanonicalPath();
report(name, burnin, mrsd, scale);
//TraceAnalysis.report(name, burnin, marginalLikelihood);
} 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, mrsd, scale);
} else if (f.getName().endsWith(".trees")) {
analyze(f, burnin, mrsd, scale);
}
}
}
}
/**
* 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
*/
private void report(String name, int burnin, double mrsd, double scale) {
int count = 0;
Map<String, List<Double>> heightMap = new HashMap<String, List<Double>>();
Set<String> states = new TreeSet<String>();
try {
FileReader fileReader = new FileReader(new File(name));
TreeImporter importer = new NexusImporter(fileReader);
while (importer.hasTree()) {
Tree tree = importer.importNextTree();
if(count>=burnin) {
for (int i = 0; i < tree.getInternalNodeCount(); i++) {
NodeRef node = tree.getInternalNode(i);
Object value = tree.getNodeAttribute(node, "state");
if (value != null) {
String state = value.toString();
List<Double> heights = heightMap.get(state);
if (heights == null) {
heights = new ArrayList<Double>();
heightMap.put(state, heights);
states.add(state);
}
double h = tree.getNodeHeight(node) * scale;
if (Double.isNaN(mrsd)) {
heights.add(h);
} else {
heights.add(mrsd - h);
}
} else {
System.out.println("Node missing state");
}
}
}
count++;
}
boolean first = true;
int maxCount = 0;
for (String state : states) {
if (first) {
first = false;
} else {
System.out.print("\t");
}
System.out.print(state);
List<Double> heights = heightMap.get(state);
if (heights.size() > maxCount) {
maxCount = heights.size();
}
}
System.out.println();
for (int i = 0; i < maxCount; i++) {
first = true;
for (String state : states) {
if (first) {
first = false;
} else {
System.out.print("\t");
}
List<Double> heights = heightMap.get(state);
if (i < heights.size()) {
System.out.print(heights.get(i));
}
}
System.out.println();
}
} catch (Importer.ImportException e) {
System.err.println("Error Parsing Input Tree: " + e.getMessage());
} catch (IOException e) {
System.err.println("Error Parsing Input Tree: " + e.getMessage());
}
}
public static void printTitle() {
System.out.println();
centreLine("NodeStateAnalyser " + 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("nodestateanalyser", "[-burnin <burnin>][<input-file-name> [<output-file-name>]]");
System.out.println();
System.out.println(" Example: nodestateanalyser test.tree");
System.out.println(" Example: nodestateanalyser -burnin 10000 trees.log out.txt");
System.out.println();
}
//Main method
public static void main(String[] args) throws IOException {
printTitle();
Arguments arguments = new Arguments(
new Arguments.Option[]{
new Arguments.IntegerOption("burnin", "the number of states to be considered as 'burn-in'"),
new Arguments.RealOption("mrsd","specifies the most recent sampling data in fractional years to rescale time [default=0]"),
new Arguments.RealOption("scale","Provide a scaling factor for the node heights [default=1]"),
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");
}
double scale = 1.0;
if (arguments.hasOption("scale")) {
scale = arguments.getRealOption("scale");
}
double mrsd = Double.NaN;
if (arguments.hasOption("mrsd")) {
mrsd = arguments.getRealOption("mrsd");
}
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("NodeStateAnalyser " + version.getVersionString() + " - Select tree 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());
}
new NodeStateAnalyser(burnin, mrsd, scale, inputFileName, outputFileName);
System.exit(0);
}
}