/*
* AncestralStatesComponentGenerator.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.beauti.components.ancestralstates;
import dr.app.beauti.generator.BaseComponentGenerator;
import dr.app.beauti.options.AbstractPartitionData;
import dr.app.beauti.options.BeautiOptions;
import dr.app.beauti.options.PartitionSubstitutionModel;
import dr.app.beauti.options.PartitionTreeModel;
import dr.app.beauti.util.XMLWriter;
import dr.evolution.datatype.DataType;
import dr.oldevomodelxml.treelikelihood.AncestralStateTreeLikelihoodParser;
import dr.util.Attribute;
/**
* @author Andrew Rambaut
* @version $Id$
*/
public class AncestralStatesComponentGenerator extends BaseComponentGenerator {
private final static boolean DEBUG = true;
private final static String DNDS_LOG_SUFFIX = ".dNdS.log";
private final static String STATE_LOG_SUFFIX = ".states.log";
public AncestralStatesComponentGenerator(final BeautiOptions options) {
super(options);
}
public boolean usesInsertionPoint(InsertionPoint point) {
AncestralStatesComponentOptions component = (AncestralStatesComponentOptions) options
.getComponentOptions(AncestralStatesComponentOptions.class);
boolean reconstructAtNodes = false;
boolean reconstructAtMRCA = false;
boolean countingStates = false;
boolean dNdSRobustCounting = false;
for (AbstractPartitionData partition : options.getDataPartitions()) {
if (component.reconstructAtNodes(partition)) reconstructAtNodes = true;
if (component.reconstructAtMRCA(partition)) reconstructAtMRCA = true;
if (component.isCountingStates(partition)) countingStates = true;
if (component.dNdSRobustCounting(partition)) dNdSRobustCounting = true;
}
if (!reconstructAtNodes && !reconstructAtMRCA && !countingStates && !dNdSRobustCounting) {
return false;
}
switch (point) {
case IN_FILE_LOG_PARAMETERS:
return countingStates || dNdSRobustCounting;
case IN_TREE_LIKELIHOOD:
return countingStates;
case IN_TREES_LOG:
return reconstructAtNodes || countingStates || dNdSRobustCounting;
case AFTER_OPERATORS:
return dNdSRobustCounting;
case AFTER_TREES_LOG:
return reconstructAtMRCA || dNdSRobustCounting;
case AFTER_MCMC:
return dNdSRobustCounting;
default:
return false;
}
}// END: usesInsertionPoint
protected void generate(final InsertionPoint point, final Object item, final String prefix, final XMLWriter writer) {
AncestralStatesComponentOptions component = (AncestralStatesComponentOptions) options
.getComponentOptions(AncestralStatesComponentOptions.class);
switch (point) {
case AFTER_OPERATORS:
writeCodonPartitionedRobustCounting(writer, component);
break;
case IN_TREE_LIKELIHOOD:
writeCountingParameter(writer, (AbstractPartitionData) item, prefix);
break;
case IN_FILE_LOG_PARAMETERS:
writeLogs(writer, component);
break;
case IN_TREES_LOG:
writeTreeLogs(writer, component, (PartitionTreeModel)item);
break;
case AFTER_TREES_LOG:
writeAncestralStateLoggers(writer, component);
break;
case AFTER_MCMC:
writeDNdSPerSiteAnalysisReport(writer, component);
break;
default:
throw new IllegalArgumentException(
"This insertion point is not implemented for "
+ this.getClass().getName());
}
}// END: generate
private void writeCountingParameter(XMLWriter writer, AbstractPartitionData partition, String prefix) {
AncestralStatesComponentOptions component = (AncestralStatesComponentOptions) options
.getComponentOptions(AncestralStatesComponentOptions.class);
if (!component.isCountingStates(partition)) {
return;
}
StringBuilder matrix = new StringBuilder();
DataType dataType = partition.getDataType();
int stateCount = dataType.getStateCount();
if (dataType.getType() == DataType.GENERAL) {
PartitionSubstitutionModel substModel = partition.getPartitionSubstitutionModel();
stateCount = substModel.getDiscreteStateSet().size();
}
for (int i = 0; i < stateCount; i++) {
for (int j = 0; j < stateCount; j++) {
if (i == j) {
matrix.append(" 0.0");
} else {
matrix.append(" 1.0");
}
}
}
writer.writeTag("parameter",
new Attribute[]{
new Attribute.Default<String>("id", partition.getPrefix() + "count"),
new Attribute.Default<String>("value", matrix.toString())},
true);
}
protected String getCommentLabel() {
return "Ancestral state reconstruction";
}
private void writeCodonPartitionedRobustCounting(XMLWriter writer,
AncestralStatesComponentOptions component) {
for (AbstractPartitionData partition : options.getDataPartitions()) {
if (component.dNdSRobustCounting(partition)) {
writeCodonPartitionedRobustCounting(writer, partition, component.isCompleteHistoryLogging(partition));
}
}
}
// Called for each model that requires robust counting (can be more than
// one)
private void writeCodonPartitionedRobustCounting(XMLWriter writer,
AbstractPartitionData partition,
boolean isCompleteHistoryLogging) {
// if (DEBUG) {
// System.err.println("DEBUG: Writing RC for " + partition.getName());
// }
writer.writeComment("Robust counting for: " + partition.getName());
// TODO: Hand coding is so 90s
String prefix = partition.getName() + ".";
// S operator
writer.writeOpenTag("codonPartitionedRobustCounting",
new Attribute[]{
new Attribute.Default<String>("id", prefix + "robustCounting1"),
new Attribute.Default<String>("labeling", "S"),
new Attribute.Default<String>("prefix", prefix),
new Attribute.Default<String>("saveCompleteHistory",
isCompleteHistoryLogging ? "true" : "false"),
new Attribute.Default<String>("useUniformization",
"true"),
new Attribute.Default<String>("unconditionedPerBranch",
"true")});
writer.writeIDref("treeModel", "treeModel");
writer.writeOpenTag("firstPosition");
writer.writeIDref("ancestralTreeLikelihood", partition.getPrefix() + "CP1.treeLikelihood");
writer.writeCloseTag("firstPosition");
writer.writeOpenTag("secondPosition");
writer.writeIDref("ancestralTreeLikelihood", partition.getPrefix() + "CP2.treeLikelihood");
writer.writeCloseTag("secondPosition");
writer.writeOpenTag("thirdPosition");
writer.writeIDref("ancestralTreeLikelihood", partition.getPrefix() + "CP3.treeLikelihood");
writer.writeCloseTag("thirdPosition");
writer.writeCloseTag("codonPartitionedRobustCounting");
writer.writeBlankLine();
// N operator:
writer.writeOpenTag("codonPartitionedRobustCounting",
new Attribute[]{
new Attribute.Default<String>("id", prefix + "robustCounting2"),
new Attribute.Default<String>("labeling", "N"),
new Attribute.Default<String>("prefix", prefix),
new Attribute.Default<String>("saveCompleteHistory",
isCompleteHistoryLogging ? "true" : "false"),
new Attribute.Default<String>("useUniformization",
"true"),
new Attribute.Default<String>("unconditionedPerBranch",
"true")});
writer.writeIDref("treeModel", "treeModel");
writer.writeOpenTag("firstPosition");
writer.writeIDref("ancestralTreeLikelihood", partition.getPrefix() + "CP1.treeLikelihood");
writer.writeCloseTag("firstPosition");
writer.writeOpenTag("secondPosition");
writer.writeIDref("ancestralTreeLikelihood", partition.getPrefix() + "CP2.treeLikelihood");
writer.writeCloseTag("secondPosition");
writer.writeOpenTag("thirdPosition");
writer.writeIDref("ancestralTreeLikelihood", partition.getPrefix() + "CP3.treeLikelihood");
writer.writeCloseTag("thirdPosition");
writer.writeCloseTag("codonPartitionedRobustCounting");
}// END: writeCodonPartitionedRobustCounting()
private void writeLogs(XMLWriter writer, AncestralStatesComponentOptions component) {
for (AbstractPartitionData partition : options.getDataPartitions()) {
if (component.dNdSRobustCounting(partition)) {
String prefix = partition.getName() + ".";
writer.writeIDref("codonPartitionedRobustCounting", prefix + "robustCounting1");
writer.writeIDref("codonPartitionedRobustCounting", prefix + "robustCounting2");
} else {
}
}
}
private void writeTreeLogs(XMLWriter writer, AncestralStatesComponentOptions component, PartitionTreeModel treeModel) {
for (AbstractPartitionData partition : options.getDataPartitions()) {
if (partition.getPartitionTreeModel() == treeModel) {
if (component.dNdSRobustCounting(partition)) {
String prefix = partition.getName() + ".";
writer.writeIDref("codonPartitionedRobustCounting", prefix + "robustCounting1");
writer.writeIDref("codonPartitionedRobustCounting", prefix + "robustCounting2");
}
if (component.reconstructAtNodes(partition)) {
// is an alignment data partition
PartitionSubstitutionModel substModel = partition.getPartitionSubstitutionModel();
int cpCount = partition.getPartitionSubstitutionModel().getCodonPartitionCount();
if (cpCount > 1) {
for (int i = 1; i <= substModel.getCodonPartitionCount(); i++) {
String prefix = partition.getPrefix() + substModel.getPrefixCodon(i);
String name = partition.getName() + "." + substModel.getPrefixCodon(i);
if (name.endsWith(".")) {
name = name.substring(0, name.length() - 1);
}
writeTrait(writer, partition, prefix, AncestralStateTreeLikelihoodParser.RECONSTRUCTION_TAG, name);
}
} else {
writeTrait(writer, partition, partition.getPrefix(), AncestralStateTreeLikelihoodParser.RECONSTRUCTION_TAG, partition.getName());
}
}
if (component.isCountingStates(partition)) {
if (partition.getDataType().getType() == DataType.CONTINUOUS) {
throw new RuntimeException("Can't do counting on Continuous data partition");
}
PartitionSubstitutionModel substModel = partition.getPartitionSubstitutionModel();
int cpCount = partition.getPartitionSubstitutionModel().getCodonPartitionCount();
if (cpCount > 1) {
for (int i = 1; i <= substModel.getCodonPartitionCount(); i++) {
String prefix = partition.getPrefix() + substModel.getPrefixCodon(i);
String name = partition.getName() + "." + substModel.getPrefixCodon(i) + "count";
writeTrait(writer, partition, prefix, "count", name);
}
} else {
writeTrait(writer, partition, partition.getPrefix(), "count", partition.getName() + ".count");
}
}
}
}
}
private void writeTrait(XMLWriter writer, AbstractPartitionData partition, String prefix, String tag, String name) {
String traitName = prefix + tag;
if (partition.getDataType().getType() == DataType.CONTINUOUS) {
traitName = partition.getName();
}
writer.writeOpenTag("trait",
new Attribute[]{
new Attribute.Default<String>("name", traitName),
new Attribute.Default<String>("tag", name)
}
);
if (partition.getDataType().getType() == DataType.CONTINUOUS) {
writer.writeIDref("multivariateTraitLikelihood", prefix + "traitLikelihood");
} else {
writer.writeIDref("ancestralTreeLikelihood", prefix + "treeLikelihood");
}
writer.writeCloseTag("trait");
}
private void writeAncestralStateLoggers(XMLWriter writer,
AncestralStatesComponentOptions component) {
for (AbstractPartitionData partition : options.getDataPartitions()) {
if (component.dNdSRobustCounting(partition)) {
writeDNdSLogger(writer, partition);
}
if (component.reconstructAtMRCA(partition)) {
writeStateLogger(writer, partition, component.getMRCATaxonSet(partition));
}
}
}
private void writeStateLogger(XMLWriter writer, AbstractPartitionData partition, String mrcaId) {
writer.writeComment("Ancestral state reconstruction for: " + partition.getName());
writer.writeOpenTag("log", new Attribute[]{
new Attribute.Default<String>("id", "fileLog_" + partition.getName()),
new Attribute.Default<String>("logEvery", Integer.toString(options.logEvery)),
new Attribute.Default<String>("fileName", options.fileNameStem + "." + partition.getName() + STATE_LOG_SUFFIX)});
PartitionSubstitutionModel substModel = partition.getPartitionSubstitutionModel();
int cpCount = partition.getPartitionSubstitutionModel().getCodonPartitionCount();
if (cpCount > 1) {
for (int i = 1; i <= substModel.getCodonPartitionCount(); i++) {
String prefix = partition.getPrefix() + substModel.getPrefixCodon(i);
String name = partition.getName() + "." + substModel.getPrefixCodon(i);
if (name.endsWith(".")) {
name = name.substring(0, name.length() - 1);
}
writeAncestralTrait(writer, partition, mrcaId, prefix, name);
}
} else {
writeAncestralTrait(writer, partition, mrcaId, partition.getPrefix(), partition.getName());
}
writer.writeCloseTag("log");
}// END: writeLogs
private void writeAncestralTrait(XMLWriter writer, AbstractPartitionData partition, String mrcaId, String prefix, String nameString) {
String traitName = prefix + AncestralStateTreeLikelihoodParser.RECONSTRUCTION_TAG;
if (partition.getDataType().getType() == DataType.CONTINUOUS) {
traitName = partition.getName();
}
writer.writeOpenTag("ancestralTrait",
new Attribute[]{
new Attribute.Default<String>("name", nameString),
new Attribute.Default<String>("traitName", traitName)
}
);
writer.writeIDref("treeModel", partition.getPartitionTreeModel().getPrefix() + "treeModel");
if (partition.getDataType().getType() == DataType.CONTINUOUS) {
writer.writeIDref("multivariateTraitLikelihood", prefix + "traitLikelihood");
} else {
writer.writeIDref("ancestralTreeLikelihood", prefix + "treeLikelihood");
}
if (mrcaId != null) {
writer.writeOpenTag("mrca");
writer.writeIDref("taxa", mrcaId);
writer.writeCloseTag("mrca");
}
writer.writeCloseTag("ancestralTrait");
}
private void writeDNdSLogger(XMLWriter writer, AbstractPartitionData partition) {
String prefix = partition.getName() + ".";
writer.writeComment("Robust counting for: " + partition.getName());
writer.writeOpenTag("log", new Attribute[]{
new Attribute.Default<String>("id", "fileLog_dNdS_" + partition.getName()),
new Attribute.Default<String>("logEvery", Integer.toString(options.logEvery)),
new Attribute.Default<String>("fileName", options.fileNameStem + "." + partition.getName() + DNDS_LOG_SUFFIX)});
writer.writeOpenTag("dNdSLogger", new Attribute[]{new Attribute.Default<String>("id",
partition.getName() + ".dNdS")});
writer.writeIDref("treeModel", "treeModel");
writer.writeIDref("codonPartitionedRobustCounting", prefix + "robustCounting1");
writer.writeIDref("codonPartitionedRobustCounting", prefix + "robustCounting2");
writer.writeCloseTag("dNdSLogger");
writer.writeCloseTag("log");
}// END: writeLogs
private void writeDNdSPerSiteAnalysisReport(XMLWriter writer,
AncestralStatesComponentOptions component) {
for (AbstractPartitionData partition : options.getDataPartitions()) {
if (component.dNdSRobustCounting(partition)) {
writeDNdSPerSiteAnalysisReport(writer, partition);
}
}
}
private void writeDNdSPerSiteAnalysisReport(XMLWriter writer,
AbstractPartitionData partition) {
writer.writeComment("Robust counting for: " + partition.getName());
writer.writeOpenTag("report");
writer.write("<dNdSPerSiteAnalysis fileName=\"" + options.fileNameStem + "." + partition.getName() + DNDS_LOG_SUFFIX + "\"/> \n");
writer.writeCloseTag("report");
}// END: writeDNdSReport
}