use of dr.evomodel.substmodel.codon.MG94K80CodonModel in project beast-mcmc by beast-dev.
the class MG94CodonModelParser method parseXMLObject.
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
Codons codons = Codons.UNIVERSAL;
if (xo.hasAttribute(GeneticCode.GENETIC_CODE)) {
String codeStr = xo.getStringAttribute(GeneticCode.GENETIC_CODE);
codons = Codons.findByName(codeStr);
}
Parameter alphaParam = (Parameter) xo.getElementFirstChild(ALPHA);
Parameter betaParam = (Parameter) xo.getElementFirstChild(BETA);
FrequencyModel freqModel = (FrequencyModel) xo.getChild(FrequencyModel.class);
boolean isParameterTotalRate = xo.getAttribute(TOTAL_RATES, true);
MG94HKYCodonModel codonModel;
if (xo.hasChildNamed(GTR_MODEL)) {
// TODO: change this into constructing a MG94HKYCodonModel (needs to be written), which is started underneath
codonModel = new MG94K80CodonModel(codons, alphaParam, betaParam, freqModel, new CodonOptions(isParameterTotalRate));
Parameter rateACValue = null;
if (xo.hasChildNamed(A_TO_C)) {
rateACValue = (Parameter) xo.getElementFirstChild(A_TO_C);
}
Parameter rateAGValue = null;
if (xo.hasChildNamed(A_TO_G)) {
rateAGValue = (Parameter) xo.getElementFirstChild(A_TO_G);
}
Parameter rateATValue = null;
if (xo.hasChildNamed(A_TO_T)) {
rateATValue = (Parameter) xo.getElementFirstChild(A_TO_T);
}
Parameter rateCGValue = null;
if (xo.hasChildNamed(C_TO_G)) {
rateCGValue = (Parameter) xo.getElementFirstChild(C_TO_G);
}
Parameter rateCTValue = null;
if (xo.hasChildNamed(C_TO_T)) {
rateCTValue = (Parameter) xo.getElementFirstChild(C_TO_T);
}
Parameter rateGTValue = null;
if (xo.hasChildNamed(G_TO_T)) {
rateGTValue = (Parameter) xo.getElementFirstChild(G_TO_T);
}
int countNull = 0;
if (rateACValue == null)
countNull++;
if (rateAGValue == null)
countNull++;
if (rateATValue == null)
countNull++;
if (rateCGValue == null)
countNull++;
if (rateCTValue == null)
countNull++;
if (rateGTValue == null)
countNull++;
if (countNull != 1)
throw new XMLParseException("Only five parameters may be specified in GTR, leave exactly one out, the others will be specifed relative to the one left out.");
if (xo.hasAttribute(KAPPA)) {
System.err.print("using GTR rates -- overrides KAPPA");
}
} else if (xo.hasChildNamed(KAPPA)) {
Parameter kappaParam = (Parameter) xo.getElementFirstChild(KAPPA);
codonModel = new MG94HKYCodonModel(codons, alphaParam, betaParam, kappaParam, freqModel, new CodonOptions(isParameterTotalRate));
// System.err.println("setting up MG94K80CodonModel");
} else {
// resort to standard MG94 without nucleotide rate bias
codonModel = new MG94K80CodonModel(codons, alphaParam, betaParam, freqModel, new CodonOptions(isParameterTotalRate));
}
if (!xo.getAttribute(NORMALIZED, true)) {
// codonModel.setNormalization(false);
// Logger.getLogger("dr.app.beagle.evomodel").info("MG94HKYCodonModel normalization: false");
}
return codonModel;
}
use of dr.evomodel.substmodel.codon.MG94K80CodonModel in project beast-mcmc by beast-dev.
the class BeagleSeqSimTest method simulateCodon.
// END: simulateAminoAcid
static void simulateCodon() {
try {
boolean calculateLikelihood = true;
System.out.println("Test case 6: simulate codons");
MathUtils.setSeed(666);
int sequenceLength = 10;
ArrayList<Partition> partitionsList = new ArrayList<Partition>();
// create tree
NewickImporter importer = new NewickImporter("(SimSeq1:73.7468,(SimSeq2:25.256989999999995,SimSeq3:45.256989999999995):18.48981);");
Tree tree = importer.importTree(null);
DefaultTreeModel treeModel = new DefaultTreeModel(tree);
// create site model
GammaSiteRateModel siteRateModel = new GammaSiteRateModel("siteModel");
// create branch rate model
BranchRateModel branchRateModel = new DefaultBranchRateModel();
// create Frequency Model
Parameter freqs = new Parameter.Default(Utils.UNIFORM_CODON_FREQUENCIES);
FrequencyModel freqModel = new FrequencyModel(Codons.UNIVERSAL, freqs);
// create substitution model
Parameter alpha = new Parameter.Default(1, 10);
Parameter beta = new Parameter.Default(1, 5);
// Parameter kappa = new Parameter.Default(1, 1);
MG94HKYCodonModel mg94 = new MG94K80CodonModel(Codons.UNIVERSAL, alpha, beta, freqModel, new CodonOptions());
HomogeneousBranchModel substitutionModel = new HomogeneousBranchModel(mg94);
// create partition
Partition partition1 = new //
Partition(//
treeModel, //
substitutionModel, //
siteRateModel, //
branchRateModel, //
freqModel, // from
0, // to
sequenceLength - 1, // every
1);
partitionsList.add(partition1);
// feed to sequence simulator and generate data
BeagleSequenceSimulator simulator = new BeagleSequenceSimulator(partitionsList);
Alignment alignment = simulator.simulate(simulateInPar, false);
System.out.println(alignment.toString());
if (calculateLikelihood) {
// NewBeagleSequenceLikelihood nbtl = new
// NewBeagleSequenceLikelihood(alignment, treeModel,
// substitutionModel, (SiteModel) siteRateModel,
// branchRateModel, null, false,
// PartialsRescalingScheme.DEFAULT);
ConvertAlignment convert = new ConvertAlignment(Nucleotides.INSTANCE, GeneticCode.UNIVERSAL, alignment);
BeagleTreeLikelihood nbtl = new //
BeagleTreeLikelihood(//
convert, //
treeModel, //
substitutionModel, //
siteRateModel, //
branchRateModel, //
null, //
false, PartialsRescalingScheme.DEFAULT, true);
System.out.println("likelihood = " + nbtl.getLogLikelihood());
}
} catch (Exception e) {
e.printStackTrace();
System.exit(-1);
}
// END: try-catch
}
use of dr.evomodel.substmodel.codon.MG94K80CodonModel in project beast-mcmc by beast-dev.
the class LineageSpecificBranchModel method main.
// END: acceptState
public static void main(String[] args) {
try {
// the seed of the BEAST
MathUtils.setSeed(666);
// create tree
NewickImporter importer = new NewickImporter("(SimSeq1:73.7468,(SimSeq2:25.256989999999995,SimSeq3:45.256989999999995):18.48981);");
TreeModel tree = new DefaultTreeModel(importer.importTree(null));
// create site model
GammaSiteRateModel siteRateModel = new GammaSiteRateModel("siteModel");
// create branch rate model
BranchRateModel branchRateModel = new DefaultBranchRateModel();
int sequenceLength = 10;
ArrayList<Partition> partitionsList = new ArrayList<Partition>();
// create Frequency Model
Parameter freqs = new Parameter.Default(new double[] { //
0.0163936, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344, //
0.01639344 });
FrequencyModel freqModel = new FrequencyModel(Codons.UNIVERSAL, freqs);
// create substitution model
Parameter alpha = new Parameter.Default(1, 10);
Parameter beta = new Parameter.Default(1, 5);
MG94HKYCodonModel mg94 = new MG94K80CodonModel(Codons.UNIVERSAL, alpha, beta, freqModel, new CodonOptions());
HomogeneousBranchModel substitutionModel = new HomogeneousBranchModel(mg94);
// create partition
Partition partition1 = new //
Partition(//
tree, //
substitutionModel, //
siteRateModel, //
branchRateModel, //
freqModel, // from
0, // to
sequenceLength - 1, // every
1);
partitionsList.add(partition1);
// feed to sequence simulator and generate data
BeagleSequenceSimulator simulator = new BeagleSequenceSimulator(partitionsList);
Alignment alignment = simulator.simulate(false, false);
ConvertAlignment convert = new ConvertAlignment(Nucleotides.INSTANCE, GeneticCode.UNIVERSAL, alignment);
List<SubstitutionModel> substModels = new ArrayList<SubstitutionModel>();
for (int i = 0; i < 2; i++) {
// alpha = new Parameter.Default(1, 10 );
// beta = new Parameter.Default(1, 5 );
// mg94 = new MG94HKYCodonModel(Codons.UNIVERSAL, alpha, beta,
// freqModel);
substModels.add(mg94);
}
Parameter uCategories = new Parameter.Default(2, 0);
// CountableBranchCategoryProvider provider = new CountableBranchCategoryProvider.IndependentBranchCategoryModel(tree, uCategories);
LineageSpecificBranchModel branchSpecific = new // provider,
LineageSpecificBranchModel(// provider,
tree, // provider,
freqModel, // provider,
substModels, uCategories);
BeagleTreeLikelihood like = new //
BeagleTreeLikelihood(//
convert, //
tree, //
branchSpecific, //
siteRateModel, //
branchRateModel, //
null, //
false, PartialsRescalingScheme.DEFAULT, true);
BeagleTreeLikelihood gold = new //
BeagleTreeLikelihood(//
convert, //
tree, //
substitutionModel, //
siteRateModel, //
branchRateModel, //
null, //
false, PartialsRescalingScheme.DEFAULT, true);
System.out.println("likelihood (gold) = " + gold.getLogLikelihood());
System.out.println("likelihood = " + like.getLogLikelihood());
} catch (Exception e) {
e.printStackTrace();
}
}
Aggregations