本文整理汇总了Java中beast.evolution.likelihood.TreeLikelihood.getPatternLogLikelihoods方法的典型用法代码示例。如果您正苦于以下问题：Java TreeLikelihood.getPatternLogLikelihoods方法的具体用法？Java TreeLikelihood.getPatternLogLikelihoods怎么用？Java TreeLikelihood.getPatternLogLikelihoods使用的例子？那么, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类beast.evolution.likelihood.TreeLikelihood的用法示例。
在下文中一共展示了TreeLikelihood.getPatternLogLikelihoods方法的2个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Java代码示例。
示例1: testMarginalisationOfLikelihoodBinary
import beast.evolution.likelihood.TreeLikelihood; //导入方法依赖的package包/类
@Test
public void testMarginalisationOfLikelihoodBinary() throws Exception {
// test summation over all patterns adds to 1 for binary data
Sequence German_ST = new Sequence("German_ST", " 10110010");
Sequence Dutch_List = new Sequence("Dutch_List", " 11010100");
Sequence English_ST = new Sequence("English_ST", " 11101000");
Alignment data = new Alignment();
data.initByName("sequence", German_ST, "sequence", Dutch_List, "sequence", English_ST,
"dataType", "binary"
);
Tree tree = BEASTTestCase.getTree(data, "(English_ST:0.22743347188019544,(German_ST:0.10557648379843088,Dutch_List:0.10557648379843088):0.12185698808176457):0.0;");
RealParameter frequencies = new RealParameter("0.683 0.317");
Frequencies freqs = new Frequencies();
freqs.initByName("frequencies", frequencies);
GeneralSubstitutionModel covarion = new GeneralSubstitutionModel();
covarion.initByName("frequencies", freqs, "rates", new RealParameter("1.0 1.0"));
SiteModel siteModel = new SiteModel();
siteModel.initByName("mutationRate", "1.0", "gammaCategoryCount", 1, "substModel", covarion);
TreeLikelihood likelihood = newTreeLikelihood();
likelihood.initByName("data", data, "tree", tree, "siteModel", siteModel);
likelihood.initByName("useAmbiguities", false, "data", data, "tree", tree, "siteModel", siteModel);
likelihood.calculateLogP();
double [] logPs = likelihood.getPatternLogLikelihoods();
double P = 0;
for (double d : logPs) {
P += Math.exp(d);
}
assertEquals(P, 1.0, BEASTTestCase.PRECISION);
}
示例2: testMarginalisationOfLikelihoodNucleotide
import beast.evolution.likelihood.TreeLikelihood; //导入方法依赖的package包/类
@Test
public void testMarginalisationOfLikelihoodNucleotide() throws Exception {
// test summation over all patterns adds to 1 for nucleotide data
Sequence German_ST = new Sequence("German_ST", " AAAAAAAAAAAAAAAA CCCCCCCCCCCCCCCC GGGGGGGGGGGGGGGG TTTTTTTTTTTTTTTT");
Sequence Dutch_List = new Sequence("Dutch_List", " AAAACCCCGGGGTTTT AAAACCCCGGGGTTTT AAAACCCCGGGGTTTT AAAACCCCGGGGTTTT");
Sequence English_ST = new Sequence("English_ST", " ACGTACGTACGTACGT ACGTACGTACGTACGT ACGTACGTACGTACGT ACGTACGTACGTACGT");
Alignment data = new Alignment();
data.initByName("sequence", German_ST, "sequence", Dutch_List, "sequence", English_ST,
"dataType", "nucleotide"
);
Tree tree = BEASTTestCase.getTree(data, "(English_ST:0.22743347188019544,(German_ST:0.10557648379843088,Dutch_List:0.10557648379843088):0.12185698808176457):0.0;");
RealParameter frequencies = new RealParameter("0.2 0.3 0.4 0.1");
Frequencies freqs = new Frequencies();
freqs.initByName("frequencies", frequencies);
GeneralSubstitutionModel gsm = new GeneralSubstitutionModel();
gsm.initByName("rates", "1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0", "frequencies", freqs);
SiteModel siteModel = new SiteModel();
siteModel.initByName("mutationRate", "1.0", "gammaCategoryCount", 1, "substModel", gsm);
TreeLikelihood likelihood = newTreeLikelihood();
likelihood.initByName("data", data, "tree", tree, "siteModel", siteModel);
likelihood.initByName("useAmbiguities", false, "data", data, "tree", tree, "siteModel", siteModel);
likelihood.calculateLogP();
double [] logPs = likelihood.getPatternLogLikelihoods();
double P = 0;
for (double d : logPs) {
P += Math.exp(d);
}
assertEquals(P, 1.0, BEASTTestCase.PRECISION);
}