/*
* SequenceErrorModelComponentGenerator.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.sequenceerror;
import dr.app.beauti.generator.BaseComponentGenerator;
import dr.app.beauti.options.AbstractPartitionData;
import dr.app.beauti.options.BeautiOptions;
import dr.app.beauti.types.SequenceErrorType;
import dr.app.beauti.util.XMLWriter;
import dr.evolution.alignment.HypermutantAlignment;
import dr.evomodel.tipstatesmodel.HypermutantErrorModel;
import dr.evomodelxml.tipstatesmodel.SequenceErrorModelParser;
import dr.evoxml.HypermutantAlignmentParser;
import dr.inference.model.ParameterParser;
import dr.inference.model.StatisticParser;
import dr.inferencexml.model.SumStatisticParser;
import dr.util.Attribute;
import dr.xml.XMLParser;
/**
* @author Andrew Rambaut
* @version $Id$
*/
public class SequenceErrorModelComponentGenerator extends BaseComponentGenerator {
SequenceErrorModelComponentGenerator(final BeautiOptions options) {
super(options);
}
public boolean usesInsertionPoint(final InsertionPoint point) {
SequenceErrorModelComponentOptions comp = (SequenceErrorModelComponentOptions) options.getComponentOptions(SequenceErrorModelComponentOptions.class);
if (!comp.usingSequenceErrorModel()) {
return false;
}
switch (point) {
case AFTER_PATTERNS:
case AFTER_SITE_MODEL:
case IN_TREE_LIKELIHOOD:
case IN_FILE_LOG_PARAMETERS:
return true;
}
return false;
}
protected void generate(final InsertionPoint point, final Object item, final String prefix, final XMLWriter writer) {
SequenceErrorModelComponentOptions component = (SequenceErrorModelComponentOptions) options.getComponentOptions(SequenceErrorModelComponentOptions.class);
switch (point) {
case AFTER_PATTERNS:
writeHypermutationAlignments(writer, component);
break;
case AFTER_SITE_MODEL:
writeErrorModels(writer, component);
break;
case IN_TREE_LIKELIHOOD:
AbstractPartitionData partition = (AbstractPartitionData) item;
SequenceErrorType errorType = component.getSequenceErrorType(partition);
if (errorType != SequenceErrorType.NO_ERROR) {
writer.writeIDref(SequenceErrorModelParser.SEQUENCE_ERROR_MODEL, partition.getPrefix() + "errorModel");
}
break;
case IN_FILE_LOG_PARAMETERS:
writeLogParameters(writer, component);
break;
default:
throw new IllegalArgumentException("This insertion point is not implemented for " + this.getClass().getName());
}
}
protected String getCommentLabel() {
return "Sequence Error Model";
}
private void writeHypermutationAlignments(XMLWriter writer, SequenceErrorModelComponentOptions component) {
for (AbstractPartitionData partition : options.getDataPartitions()) {
String prefix = partition.getPrefix();//partition.getName() + ".";
if (component.isHypermutation(partition)) {
SequenceErrorType errorType = component.getSequenceErrorType(partition);
final String errorTypeName;
switch (errorType) {
case HYPERMUTATION_ALL:
errorTypeName = HypermutantAlignment.APOBECType.ALL.toString();
break;
case HYPERMUTATION_BOTH:
errorTypeName = HypermutantAlignment.APOBECType.BOTH.toString();
break;
case HYPERMUTATION_HA3F:
errorTypeName = HypermutantAlignment.APOBECType.HA3F.toString();
break;
case HYPERMUTATION_HA3G:
errorTypeName = HypermutantAlignment.APOBECType.HA3G.toString();
break;
default:
throw new RuntimeException("Unknown ErrorModelType: " + errorType.toString());
}
writer.writeOpenTag(
HypermutantAlignmentParser.HYPERMUTANT_ALIGNMENT,
new Attribute[]{
new Attribute.Default<String>(XMLParser.ID, prefix + "hypermutants"),
new Attribute.Default<String>("type", errorTypeName)
}
);
writer.writeIDref("alignment", partition.getTaxonList().getId());
writer.writeCloseTag(HypermutantAlignmentParser.HYPERMUTANT_ALIGNMENT);
}
}
}
private void writeErrorModels(XMLWriter writer, SequenceErrorModelComponentOptions component) {
for (AbstractPartitionData partition : options.getDataPartitions()) {
String prefix = partition.getPrefix();//partition.getName() + ".";
SequenceErrorType errorType = component.getSequenceErrorType(partition);
if (component.isHypermutation(partition)) {
writer.writeOpenTag(
HypermutantErrorModel.HYPERMUTANT_ERROR_MODEL,
new Attribute[]{
new Attribute.Default<String>(XMLParser.ID, prefix + SequenceErrorModelComponentOptions.ERROR_MODEL)
}
);
writer.writeIDref(HypermutantAlignmentParser.HYPERMUTANT_ALIGNMENT, prefix + "hypermutants");
writeParameter(HypermutantErrorModel.HYPERMUTATION_RATE, prefix + SequenceErrorModelComponentOptions.HYPERMUTION_RATE_PARAMETER, 1, writer);
writeParameter(HypermutantErrorModel.HYPERMUTATION_INDICATORS, prefix + SequenceErrorModelComponentOptions.HYPERMUTANT_INDICATOR_PARAMETER, 1, writer);
writer.writeCloseTag(HypermutantErrorModel.HYPERMUTANT_ERROR_MODEL);
writer.writeOpenTag(SumStatisticParser.SUM_STATISTIC, new Attribute[]{
new Attribute.Default<String>(XMLParser.ID, prefix + SequenceErrorModelComponentOptions.HYPERMUTANT_COUNT_STATISTIC),
new Attribute.Default<Boolean>(SumStatisticParser.ELEMENTWISE, true)});
writer.writeIDref(ParameterParser.PARAMETER, prefix + SequenceErrorModelComponentOptions.HYPERMUTANT_INDICATOR_PARAMETER);
writer.writeCloseTag(SumStatisticParser.SUM_STATISTIC);
} else if (errorType != SequenceErrorType.NO_ERROR) {
final String errorTypeName = (errorType == SequenceErrorType.AGE_TRANSITIONS ||
errorType == SequenceErrorType.BASE_TRANSITIONS ?
"transitions" : "all");
writer.writeOpenTag(
SequenceErrorModelParser.SEQUENCE_ERROR_MODEL,
new Attribute[]{
new Attribute.Default<String>(XMLParser.ID, prefix + SequenceErrorModelComponentOptions.ERROR_MODEL),
new Attribute.Default<String>("type", errorTypeName)
}
);
if (component.hasAgeDependentRate(partition)) {
writeParameter(SequenceErrorModelComponentOptions.AGE_RATE, prefix + SequenceErrorModelComponentOptions.AGE_RATE_PARAMETER, 1, writer);
}
if (component.hasBaseRate(partition)) {
writeParameter(SequenceErrorModelComponentOptions.BASE_RATE, prefix + SequenceErrorModelComponentOptions.BASE_RATE_PARAMETER, 1, writer);
}
writer.writeCloseTag(SequenceErrorModelParser.SEQUENCE_ERROR_MODEL);
}
}
}
private void writeLogParameters(final XMLWriter writer, final SequenceErrorModelComponentOptions component) {
for (AbstractPartitionData partition : options.getDataPartitions()) {
String prefix = partition.getPrefix();//partition.getName() + ".";
SequenceErrorType errorType = component.getSequenceErrorType(partition);
if (errorType != SequenceErrorType.NO_ERROR) {
if (component.isHypermutation(partition)) {
writer.writeIDref(ParameterParser.PARAMETER, prefix + SequenceErrorModelComponentOptions.HYPERMUTION_RATE_PARAMETER);
writer.writeIDref(StatisticParser.STATISTIC, prefix + SequenceErrorModelComponentOptions.HYPERMUTANT_COUNT_STATISTIC);
writer.writeOpenTag(StatisticParser.STATISTIC,
new Attribute.Default<String>("name", "isHypermutated"));
writer.writeIDref(HypermutantErrorModel.HYPERMUTANT_ERROR_MODEL,
prefix + SequenceErrorModelComponentOptions.ERROR_MODEL);
writer.writeCloseTag(StatisticParser.STATISTIC);
}
if (component.hasAgeDependentRate(partition)) {
writer.writeIDref(ParameterParser.PARAMETER, prefix + SequenceErrorModelComponentOptions.AGE_RATE_PARAMETER);
}
if (component.hasBaseRate(partition)) {
writer.writeIDref(ParameterParser.PARAMETER, prefix + SequenceErrorModelComponentOptions.BASE_RATE_PARAMETER);
}
}
}
}
}