/*
* PCACodonModelParser.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.oldevomodelxml.substmodel;
import java.util.logging.Logger;
import dr.evolution.datatype.Codons;
import dr.evolution.datatype.DataType;
import dr.evolution.datatype.GeneticCode;
import dr.evomodel.substmodel.*;
import dr.inference.model.Parameter;
import dr.oldevomodel.substmodel.AbstractPCARateMatrix;
import dr.oldevomodel.substmodel.FrequencyModel;
import dr.oldevomodel.substmodel.PCACodonModel;
import dr.oldevomodel.substmodel.PCARateMatrixMammalia;
import dr.xml.*;
/**
* XML parser for PCACodonModel
*
* @author Stefan Zoller
*/
public class PCACodonModelParser extends AbstractXMLObjectParser {
public static final String PCA_CODON_MODEL = "pcaCodonModel";
public static final String PCATYPE = "pcaType";
public static final String PCANUMBER = "pcaNumber";
public static final String PCA_DIMENSION = "pcaDimension";
public static final String PCA_DATA_DIR = "pcaDataDir";
public String getParserName() { return PCA_CODON_MODEL; }
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
Codons codons = Codons.UNIVERSAL;
if (xo.hasAttribute(GeneticCode.GENETIC_CODE)) {
String codeStr = xo.getStringAttribute(GeneticCode.GENETIC_CODE);
if (codeStr.equals(GeneticCode.UNIVERSAL.getName())) {
codons = Codons.UNIVERSAL;
} else if (codeStr.equals(GeneticCode.VERTEBRATE_MT.getName())) {
codons = Codons.VERTEBRATE_MT;
} else if (codeStr.equals(GeneticCode.YEAST.getName())) {
codons = Codons.YEAST;
} else if (codeStr.equals(GeneticCode.MOLD_PROTOZOAN_MT.getName())) {
codons = Codons.MOLD_PROTOZOAN_MT;
} else if (codeStr.equals(GeneticCode.INVERTEBRATE_MT.getName())) {
codons = Codons.INVERTEBRATE_MT;
} else if (codeStr.equals(GeneticCode.CILIATE.getName())) {
codons = Codons.CILIATE;
} else if (codeStr.equals(GeneticCode.ECHINODERM_MT.getName())) {
codons = Codons.ECHINODERM_MT;
} else if (codeStr.equals(GeneticCode.EUPLOTID_NUC.getName())) {
codons = Codons.EUPLOTID_NUC;
} else if (codeStr.equals(GeneticCode.BACTERIAL.getName())) {
codons = Codons.BACTERIAL;
} else if (codeStr.equals(GeneticCode.ALT_YEAST.getName())) {
codons = Codons.ALT_YEAST;
} else if (codeStr.equals(GeneticCode.ASCIDIAN_MT.getName())) {
codons = Codons.ASCIDIAN_MT;
} else if (codeStr.equals(GeneticCode.FLATWORM_MT.getName())) {
codons = Codons.FLATWORM_MT;
} else if (codeStr.equals(GeneticCode.BLEPHARISMA_NUC.getName())) {
codons = Codons.BLEPHARISMA_NUC;
} else if (codeStr.equals(GeneticCode.NO_STOPS.getName())) {
codons = Codons.NO_STOPS;
}
}
// get number of PCs
Parameter pcaDimensionParameter = (Parameter)xo.getElementFirstChild(PCA_DIMENSION);
// get directory with pca rate matrix files; fallback to default "pcadata"
String dirString = "pcadata";
if(xo.hasAttribute(PCA_DATA_DIR)) {
dirString = xo.getStringAttribute(PCA_DATA_DIR);
}
// get type of rate matrix; fallback to mammalia pca
AbstractPCARateMatrix pcaType = new PCARateMatrixMammalia(pcaDimensionParameter.getDimension(), dirString);
// check for other type of pca
if(xo.hasAttribute(PCATYPE)) {
String pcaTypeString = xo.getStringAttribute(PCATYPE);
if(pcaTypeString.equals(PCARateMatrixMammalia.getName())) {
pcaType = new PCARateMatrixMammalia(pcaDimensionParameter.getDimension(), dirString);
}
}
// decide if getting frequencies from csv or estimating from MSA
FrequencyModel freqModel = null;
if (xo.getChild(FrequencyModel.class) != null) {
freqModel = (FrequencyModel)xo.getChild(FrequencyModel.class);
} else {
freqModel = createNewFreqModel(codons, pcaType);
}
return new PCACodonModel(codons, pcaType, pcaDimensionParameter, freqModel);
}
// read frequencies from XML and return FrequencyModel object
private FrequencyModel createNewFreqModel(DataType codons, AbstractPCARateMatrix type) throws XMLParseException {
double[] freqs = type.getFrequencies();
double sum = 0;
for (int j = 0; j < freqs.length; j++) {
sum += freqs[j];
}
if (Math.abs(sum - 1.0) > 1e-8) {
throw new XMLParseException("Frequencies do not sum to 1 (they sum to " + sum + ")");
}
FrequencyModel fm = new FrequencyModel(codons, freqs);
Logger.getLogger("dr.evomodel").info("Using frequencies from data file");
return fm;
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public String getParserDescription() {
return "This element represents the PCA model of codon evolution.";
}
public Class getReturnType() { return PCACodonModel.class; }
public XMLSyntaxRule[] getSyntaxRules() { return rules; }
private XMLSyntaxRule[] rules = new XMLSyntaxRule[] {
new StringAttributeRule(GeneticCode.GENETIC_CODE,
"The genetic code to use",
new String[] {
GeneticCode.UNIVERSAL.getName(),
GeneticCode.VERTEBRATE_MT.getName(),
GeneticCode.YEAST.getName(),
GeneticCode.MOLD_PROTOZOAN_MT.getName(),
GeneticCode.INVERTEBRATE_MT.getName(),
GeneticCode.CILIATE.getName(),
GeneticCode.ECHINODERM_MT.getName(),
GeneticCode.EUPLOTID_NUC.getName(),
GeneticCode.BACTERIAL.getName(),
GeneticCode.ALT_YEAST.getName(),
GeneticCode.ASCIDIAN_MT.getName(),
GeneticCode.FLATWORM_MT.getName(),
GeneticCode.BLEPHARISMA_NUC.getName(),
GeneticCode.NO_STOPS.getName()}, true),
new StringAttributeRule(PCATYPE,
"The PCA type to use",
new String[] {
PCARateMatrixMammalia.getName(),
}, true),
new StringAttributeRule(PCA_DATA_DIR,
"The directory with the PCA data files",
"pcadata", true),
new ElementRule(PCA_DIMENSION,
new XMLSyntaxRule[] { new ElementRule(Parameter.class) }),
new ElementRule(FrequencyModel.class, true)
};
}