/*
* CompleteHistoryLogger.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.treelikelihood.utilities;
import dr.evomodel.treelikelihood.MarkovJumpsBeagleTreeLikelihood;
import dr.evomodel.treelikelihood.MarkovJumpsTraitProvider;
import dr.evolution.tree.NodeRef;
import dr.evolution.tree.Tree;
import dr.evolution.tree.TreeTrait;
import dr.inference.loggers.LogColumn;
import dr.inference.loggers.Loggable;
import dr.inference.markovjumps.StateHistory;
import dr.util.Citable;
import dr.util.Citation;
import dr.util.CommonCitations;
import java.awt.*;
import java.io.Serializable;
import java.util.*;
import java.util.List;
import java.util.logging.Logger;
/**
* A class to conveniently log a complete state history of a continuous-time Markov chain along a tree
* simulated using the Uniformization Method
* <p/>
* This work is supported by NSF grant 0856099
* <p/>
* Minin VN and Suchard MA (2008) Counting labeled transitions in continous-time Markov models of evolution.
* Journal of Mathematical Biology, 56, 391-412.
* <p/>
* Rodrigue N, Philippe H and Lartillot N (2006) Uniformization for sampling realizations of Markov processes:
* applications to Bayesian implementations of codon substitution models. Bioinformatics, 24, 56-62.
* <p/>
* Hobolth A and Stone E (2009) Simulation from endpoint-conditioned, continuous-time Markov chains on a finite
* state space, with applications to molecular evolution. Annals of Applied Statistics, 3, 1204-1231.
*
* @author Marc A. Suchard
* @author Philippe Lemey
* @author Andrew Rambaut
*/
public class CompleteHistoryLogger implements Loggable, Citable {
public static final String TOTAL_COUNT_NAME = "totalChangeCount";
public static final String COMPLETE_HISTORY_NAME = "completeHistory";
public CompleteHistoryLogger(MarkovJumpsTraitProvider treeLikelihood, HistoryFilter filter) {
this.tree = treeLikelihood.getTreeModel();
this.patternCount = treeLikelihood.getPatternCount();
treeTraitHistory = new TreeTrait[patternCount];
for (int site = 0; site < patternCount; ++site) {
String traitName = (patternCount == 1) ? MarkovJumpsBeagleTreeLikelihood.HISTORY : MarkovJumpsBeagleTreeLikelihood.HISTORY + "_" + (site + 1);
treeTraitHistory[site] = treeLikelihood.getTreeTrait(traitName);
if (treeTraitHistory[site] == null) {
throw new RuntimeException("Tree '" + treeLikelihood.getId() + "' does not have a complete history trait at site " + (site + 1));
}
}
treeTraitCount = treeLikelihood.getTreeTrait(MarkovJumpsBeagleTreeLikelihood.TOTAL_COUNTS);
if (treeTraitCount == null) {
throw new RuntimeException("No sum");
}
if (filter == null) {
this.filter = new HistoryFilter.Default();
} else {
this.filter = filter;
Logger.getLogger("dr.app.beagle").info("\tWith filter: " + filter.getDescription() + "\n");
}
}
private static int parseListString(String listString, int currentOffset, List list) {
while (currentOffset < listString.length()) {
// Skip leading separators
if (listString.startsWith(",", currentOffset)) {
currentOffset++;
}
if (listString.startsWith("{", currentOffset)) {
// Need to make a new list
List newList = new ArrayList();
currentOffset = parseListString(listString, currentOffset + 1, newList);
list.add(newList);
} else if (listString.startsWith("}", currentOffset)) {
// the list is ended
return currentOffset + 1;
} else {
// Parse until next ',' or '}'
int nextComma = listString.indexOf(",", currentOffset);
int nextClose = listString.indexOf("}", currentOffset);
if (nextComma < 0) nextComma = listString.length() - 1;
if (nextClose < 0) nextClose = listString.length() - 1;
int nextOffset = Math.min(nextComma, nextClose);
list.add(listString.substring(currentOffset, nextOffset).trim());
currentOffset = nextOffset;
}
}
return currentOffset;
}
public static Serializable parseValue(String value) {
List nestedParse = new ArrayList<Object>();
parseListString(value, 0, nestedParse);
return parseValueObject(nestedParse.get(0));
}
private static Serializable parseValueObject(Object objValue) {
if (objValue instanceof List) {
List newObjList = (List) objValue;
Object[] newObjects = new Object[newObjList.size()];
for (int i = 0; i < newObjList.size(); ++i) {
newObjects[i] = parseValueObject(newObjList.get(i));
}
return newObjects;
}
String value = (String) objValue;
if (value.startsWith("#")) {
// I am not sure whether this is a good idea but
// I am going to assume that a # denotes an RGB colour
try {
return Color.decode(value.substring(1));
} catch (NumberFormatException nfe1) {
// not a colour
}
}
if (value.equalsIgnoreCase("TRUE") || value.equalsIgnoreCase("FALSE")) {
return Boolean.valueOf(value);
}
// Attempt to format the value as an integer
try {
return new Integer(value);
} catch (NumberFormatException nfe1) {
// not an integer
}
// Attempt to format the value as a double
try {
return new Double(value);
} catch (NumberFormatException nfe2) {
// not a double
}
// return the trimmed string
return value;
}
public void setFilter(HistoryFilter filter) {
this.filter = filter;
}
public LogColumn[] getColumns() {
LogColumn[] columns = new LogColumn[1 + patternCount];
columns[0] = new LogColumn.Abstract(TOTAL_COUNT_NAME) {
@Override
protected String getFormattedValue() {
return treeTraitCount.getTraitString(tree, null);
}
};
for (int site = 0; site < patternCount; ++site) {
String name = (patternCount == 0) ? COMPLETE_HISTORY_NAME : COMPLETE_HISTORY_NAME + "_" + (site + 1);
final int anonSite = site;
columns[1 + site] = new LogColumn.Abstract(name) {
@Override
protected String getFormattedValue() {
boolean empty = true;
StringBuilder bf = new StringBuilder("{");
int count = 0;
for (int i = 0; i < tree.getNodeCount(); ++i) {
NodeRef node = tree.getNode(i);
if (!tree.isRoot(node)) {
NodeRef parent = tree.getParent(node);
double parentTime = tree.getNodeHeight(parent);
double childTime = tree.getNodeHeight(node);
double minTime = Math.min(parentTime, childTime);
double maxTime = Math.max(parentTime, childTime);
String trait = treeTraitHistory[anonSite].getTraitString(tree, node);
if (trait != null && trait.compareTo("{}") != 0) {
Object[] changes = (Object[]) parseValue(trait);
for (int j = 0; j < changes.length; ++j) {
Object[] change = (Object[]) changes[j];
int offset = (change.length == 4) ? 1 : 0;
String source = (String) change[1 + offset];
String dest = (String) change[2 + offset];
double thisTime = (Double) change[0 + offset];
if (thisTime < 0.0) {
throw new RuntimeException("negative time");
}
if (thisTime > maxTime || thisTime < minTime) {
throw new RuntimeException("Invalid simulation time");
}
// TODO Delegate to Filter(source, dest, thisTime). If filtered then
boolean filtered = filter.filter(source, dest, thisTime);
if (filtered) {
if (!empty) {
bf.append(",");
}
StateHistory.addEventToStringBuilder(bf, source, dest,
thisTime, anonSite + 1);
count++;
empty = false;
} else {
// Do nothing
}
}
}
}
}
bf.append("}").append(" ").append(count);
return bf.toString();
}
};
}
return columns;
}
@Override
public Citation.Category getCategory() {
return Citation.Category.COUNTING_PROCESSES;
}
@Override
public String getDescription() {
return "Complete history logger";
}
public List<Citation> getCitations() {
return Arrays.asList(//CommonCitations.LEMEY_2012, // TODO Find published Lemey paper
CommonCitations.MININ_2008_FAST, CommonCitations.BLOOM_2013_STABILITY);
}
final private Tree tree;
final private TreeTrait[] treeTraitHistory;
final private TreeTrait treeTraitCount;
final private int patternCount;
private HistoryFilter filter;
}