Java Codons.UNIVERSAL属性代码示例

本文整理汇总了Java中dr.evolution.datatype.Codons.UNIVERSAL属性的典型用法代码示例。如果您正苦于以下问题：Java Codons.UNIVERSAL属性的具体用法？Java Codons.UNIVERSAL怎么用？Java Codons.UNIVERSAL使用的例子？那么, 这里精选的属性代码示例或许可以为您提供帮助。您也可以进一步了解该属性所在类dr.evolution.datatype.Codons的用法示例。

在下文中一共展示了Codons.UNIVERSAL属性的15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: testCodonSimulation

public void testCodonSimulation() {
    Parameter kappa = new Parameter.Default(1, 2.0);
    Parameter omega = new Parameter.Default(1, 5.0); // Expect many more non-syn changes

    Codons codons = Codons.UNIVERSAL;
    int stateCount = codons.getStateCount();
    double[] p = new double[stateCount];
    for (int i = 0; i < stateCount; i++) {
        p[i] = 1.0 / (double) stateCount;
    }
    Parameter pi = new Parameter.Default(p);
    FrequencyModel f = new FrequencyModel(codons, pi);
    GY94CodonModel codonModel = new GY94CodonModel(codons, omega, kappa, f);

    Parameter mu = new Parameter.Default(1, 0.5);
    Parameter alpha = new Parameter.Default(1, 0.5);
    GammaSiteRateModel siteModel = new GammaSiteRateModel("gammaModel", mu, alpha, 4, null);
    siteModel.setSubstitutionModel(codonModel);
    BranchRateModel branchRateModel = new DefaultBranchRateModel();

    double analyticResult = TreeUtils.getTreeLength(tree, tree.getRoot()) * mu.getParameterValue(0);
    int nSites = 100;

    double[] synRegMatrix = CodonLabeling.getRegisterMatrix(CodonLabeling.SYN, codons, false); // use base 61
    double[] nonSynRegMatrix = CodonLabeling.getRegisterMatrix(CodonLabeling.NON_SYN, codons, false); // use base 61

    runSimulation(tree, siteModel, branchRateModel, nSites,
            new double[][] {synRegMatrix, nonSynRegMatrix}, analyticResult);

}

开发者ID:beast-dev，项目名称:beast-mcmc，代码行数:30，代码来源:CompleteHistorySimulatorTest.java

示例2: main

public static void main(String[] args) {
        GY94CodonModel codonModel = new GY94CodonModel(Codons.UNIVERSAL,
                new Parameter.Default(1.0), new Parameter.Default(2.0),
                new FrequencyModel(Codons.UNIVERSAL, new Parameter.Default(61, 1.0 / 61.0)));
        EigenDecomposition ed1 = codonModel.getEigenDecomposition();
//        double[][] q = codonModel.getQ();

//        System.err.println("matrixQ = \n"+codonModel.printQ());// new Matrix(q));
        FrequencyModel freqModel = new FrequencyModel(HiddenCodons.UNIVERSAL_HIDDEN_2, new Parameter.Default(122, 1.0 / 122.0));
        System.err.println("freq = " + new Vector(freqModel.getFrequencies()));
//        System.exit(-1);
        MarkovModulatedGY94CodonModel mmCodonModel = new MarkovModulatedGY94CodonModel(HiddenCodons.UNIVERSAL_HIDDEN_2,
                new Parameter.Default(2, 5.0), new Parameter.Default(2, 1.0),
                new Parameter.Default(2.0), freqModel
        );
        EigenDecomposition ed2 = mmCodonModel.getEigenDecomposition();
        System.err.println("matrixQ = \n" + mmCodonModel.printQ());// new Matrix(q));
    }

开发者ID:beast-dev，项目名称:beast-mcmc，代码行数:18，代码来源:MarkovModulatedGY94CodonModel.java

示例3: getCodonPartitionedRobustCountings

private static RootConditionedCodonPartitionedRobustCounting[] getCodonPartitionedRobustCountings(final TreeModel treeModel, final AncestralStateBeagleTreeLikelihood[] treeLikelihoods) {
    RootConditionedCodonPartitionedRobustCounting[] robustCounts = new RootConditionedCodonPartitionedRobustCounting[2];

    String[] type = new String[]{"S", "N"};
    StratifiedTraitOutputFormat branchFormat = StratifiedTraitOutputFormat.SUM_OVER_SITES;
    StratifiedTraitOutputFormat logFormat = StratifiedTraitOutputFormat.SUM_OVER_SITES;
    for (int i = 0; i < 2; i++) {
        robustCounts[i] = new RootConditionedCodonPartitionedRobustCounting(
                type[i],
                treeModel,
                treeLikelihoods,
                Codons.UNIVERSAL,
                CodonLabeling.parseFromString(type[i]),
                true,  // uniformization
                true,  // external branches
                true,  // internal branches
                true,  // unconditional per branch
                false, // complete history
                branchFormat,
                logFormat);
    }
    return robustCounts;
}

开发者ID:cmccoy，项目名称:startreerenaissance，代码行数:23，代码来源:StarTreeRenaissance.java

示例4: 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 omegaParam = (Parameter)xo.getElementFirstChild(OMEGA);
        Parameter kappaParam = (Parameter)xo.getElementFirstChild(KAPPA);
        FrequencyModel freqModel = (FrequencyModel)xo.getChild(FrequencyModel.class);
        GY94CodonModel codonModel = new GY94CodonModel(codons, omegaParam, kappaParam, freqModel);

//            codonModel.printRateMap();

        return codonModel;
    }

开发者ID:whdc，项目名称:ieo-beast，代码行数:17，代码来源:GY94CodonModelParser.java

示例5: PCARateMatrixMammalia

/**
    * constructor
    *
    * @param nrOfPCs   Number of PCs to use
    * @param dir		Directory which includes the rate matrix csv files
    */
   public PCARateMatrixMammalia(int nrOfPCs, String dir) {
	super("mammalia", Codons.UNIVERSAL, dir);
	
	// reading data files:
	setupMeans();
	setupFreqs();
	setupScales();
	setupStartFacs();
	setupPCs(nrOfPCs);
}

开发者ID:beast-dev，项目名称:beast-mcmc，代码行数:16，代码来源:PCARateMatrixMammalia.java

示例6: createDataType

public DataType createDataType() {

		DataType dataType = null;

		if (this.dataTypeIndex == 0) { // Nucleotide

			dataType = Nucleotides.INSTANCE;

		} else if (this.dataTypeIndex == 1) { // Codon

			dataType = Codons.UNIVERSAL;

		} else if (this.dataTypeIndex == 2) { // AminoAcid

			dataType = AminoAcids.INSTANCE;
			
		} else {

			System.out.println("Not yet implemented");

		}

		return dataType;
	}

开发者ID:beast-dev，项目名称:beast-mcmc，代码行数:24，代码来源:PartitionData.java

示例7: simulateRandomBranchAssignment

static void simulateRandomBranchAssignment() {
		
		try {
			
			System.out.println("Test case I dunno which: simulate random branch assignments");

			MathUtils.setSeed(666);

			int sequenceLength = 10;
			ArrayList<Partition> partitionsList = new ArrayList<Partition>();
			
	        File treeFile = new File("/home/filip/Dropbox/BeagleSequenceSimulator/SimTree/SimTree.figtree");
	        Tree tree = Utils.importTreeFromFile(treeFile);
	        TreeModel treeModel = new TreeModel(tree);
			
			// create Frequency Model
			Parameter freqs = new Parameter.Default(Utils.UNIFORM_CODON_FREQUENCIES);
			FrequencyModel freqModel = new FrequencyModel(Codons.UNIVERSAL,
					freqs);

			// create base subst model
			Parameter omegaParameter = new Parameter.Default("omega", 1, 1.0);
			Parameter kappaParameter = new Parameter.Default("kappa", 1, 1.0);
			GY94CodonModel baseSubModel = new GY94CodonModel(Codons.UNIVERSAL, omegaParameter, kappaParameter, freqModel);
			
			RandomBranchModel substitutionModel = new RandomBranchModel(treeModel, baseSubModel, 0.25, false, -1);
			
			// create site model
			GammaSiteRateModel siteRateModel = new GammaSiteRateModel(
					"siteModel");

			// create branch rate model
			BranchRateModel branchRateModel = new DefaultBranchRateModel();

			// create partition
			Partition partition1 = new Partition(treeModel, //
					substitutionModel,//
					siteRateModel, //
					branchRateModel, //
					freqModel, //
					0, // from
					sequenceLength - 1, // to
					1 // every
			);

//			Sequence ancestralSequence = new Sequence();
//			ancestralSequence.appendSequenceString("TCAAGTGAGG");
//			partition1.setRootSequence(ancestralSequence);

			partitionsList.add(partition1);

			// feed to sequence simulator and generate data
			BeagleSequenceSimulator simulator = new BeagleSequenceSimulator(
					partitionsList);

			SimpleAlignment alignment = simulator.simulate(simulateInPar, true);

			// alignment.setOutputType(SimpleAlignment.OutputType.NEXUS);
			alignment.setOutputType(SimpleAlignment.OutputType.XML);

			System.out.println(alignment.toString());
	        
	        
		} catch (Exception e) {

			e.printStackTrace();

		}// END: try-catch
		
	}

开发者ID:beast-dev，项目名称:beast-mcmc，代码行数:70，代码来源:BeagleSeqSimTest.java

示例8: PCARateMatrixMammalia

public PCARateMatrixMammalia(int nrOfPCs, String dir) {
	super("mammalia", Codons.UNIVERSAL, dir);
	
	// reading data files
	setupMeans();
	setupFreqs();
	setupScales();
	setupStartFacs();
	setupPCs(nrOfPCs);
}

开发者ID:beast-dev，项目名称:beast-mcmc，代码行数:10，代码来源:PCARateMatrixMammalia.java

示例9: 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 omegaParameter = (Parameter)xo.getElementFirstChild(OMEGA);
        
        int dim = omegaParameter.getDimension();
        double value = omegaParameter.getParameterValue(dim - 1); 
        if(value < 0) {
        	throw new RuntimeException("Negative Omega parameter value " + value);
        }//END: negative check
        
        Parameter kappaParameter = (Parameter)xo.getElementFirstChild(KAPPA);
        
        dim = kappaParameter.getDimension();
        value = kappaParameter.getParameterValue(dim - 1);
        if(value < 0) {
        	throw new RuntimeException("Negative kappa parameter value value " + value);
        }//END: negative check
        
        FrequencyModel freqModel = (FrequencyModel)xo.getChild(FrequencyModel.class);
        GY94CodonModel codonModel = new GY94CodonModel(codons, omegaParameter, kappaParameter, freqModel);

//            codonModel.printRateMap();

        return codonModel;
    }

开发者ID:beast-dev，项目名称:beast-mcmc，代码行数:31，代码来源:GY94CodonModelParser.java

示例10: testCodonSimulation

public void testCodonSimulation() {
    Parameter kappa = new Parameter.Default(1, 2.0);
    Parameter omega = new Parameter.Default(1, 5.0); // Expect many more non-syn changes

    Codons codons = Codons.UNIVERSAL;
    int stateCount = codons.getStateCount();
    double[] p = new double[stateCount];
    for (int i = 0; i < stateCount; i++) {
        p[i] = 1.0 / (double) stateCount;
    }
    Parameter pi = new Parameter.Default(p);
    FrequencyModel f = new FrequencyModel(codons, pi);
    GY94CodonModel codonModel = new GY94CodonModel(codons, omega, kappa, f);

    Parameter mu = new Parameter.Default(1, 0.5);
    Parameter alpha = new Parameter.Default(1, 0.5);
    GammaSiteRateModel siteModel = new GammaSiteRateModel("gammaModel", mu, alpha, 4, null);
    siteModel.setSubstitutionModel(codonModel);
    BranchRateModel branchRateModel = new DefaultBranchRateModel();

    double analyticResult = Tree.Utils.getTreeLength(tree, tree.getRoot()) * mu.getParameterValue(0);
    int nSites = 100;

    double[] synRegMatrix = CodonLabeling.getRegisterMatrix(CodonLabeling.SYN, codons, false); // use base 61
    double[] nonSynRegMatrix = CodonLabeling.getRegisterMatrix(CodonLabeling.NON_SYN, codons, false); // use base 61

    runSimulation(tree, siteModel, branchRateModel, nSites,
            new double[][] {synRegMatrix, nonSynRegMatrix}, analyticResult);

}

开发者ID:whdc，项目名称:ieo-beast，代码行数:30，代码来源:CompleteHistorySimulatorTest.java

示例11: Defects

public Defects(Alignment alignment) {

        Codons codons = Codons.UNIVERSAL;
        Nucleotides nucs = Nucleotides.INSTANCE;

        Alignment codonAlignment = new ConvertAlignment(codons, alignment);

        sequenceCount = codonAlignment.getSequenceCount();

        for (int i = 0; i < codonAlignment.getSequenceCount(); i++) {
            for (int j = 0; j < codonAlignment.getSiteCount(); j++) {
                int state = codonAlignment.getState(i, j);

                if (codons.isStopCodon(state)) {
                    //System.out.print("*");
                    //    System.out.println("Found stop codon: " + triplet + " in sequence " + codonAlignment.getTaxonId(i) + " at site " + j);
                    addDefect(STOP, i, j);
                    totalReads += 1;
                } else if (codons.isGapState(state)) {
                    //System.out.print("?");
                    // go back to original alignment and check
                    int start = j*3;
                    int state1 = alignment.getState(i,start);
                    int state2 = alignment.getState(i,start+1);
                    int state3 = alignment.getState(i,start+2);
                    if (nucs.isGapState(state1) && nucs.isGapState(state2) && nucs.isGapState(state3)) {
                        // real gap
                    } else {
                        // defect
                        //    System.out.println("Found gap in sequence " + codonAlignment.getTaxonId(i) + " at site " + j);
                        addDefect(INDEL, i, j);
                        //totalReads += 1;
                    }

                } else {
                    //System.out.print(" ");
                    totalReads += 1;
                }
            }
            //System.out.println();
        }
    }

开发者ID:beast-dev，项目名称:beast-mcmc，代码行数:42，代码来源:Defects.java

示例12: 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);
            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;
            }
        }

        Parameter omegaParam = (Parameter)xo.getElementFirstChild(OMEGA);
        Parameter kappaParam = (Parameter)xo.getElementFirstChild(KAPPA);
        FrequencyModel freqModel = (FrequencyModel)xo.getChild(FrequencyModel.class);

//            codonModel.printRateMap();

        return new YangCodonModel(codons, omegaParam, kappaParam, freqModel);
    }

开发者ID:beast-dev，项目名称:beast-mcmc，代码行数:44，代码来源:YangCodonModelParser.java

示例13: 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);
            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);
    }

开发者ID:beast-dev，项目名称:beast-mcmc，代码行数:65，代码来源:PCACodonModelParser.java

示例14: 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);
            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);
    }

开发者ID:beast-dev，项目名称:beast-mcmc，代码行数:65，代码来源:PCACodonModelParser.java

示例15: setUp

public void setUp() {
    codons = Codons.UNIVERSAL;
    geneticCode = codons.getGeneticCode();
}

开发者ID:beast-dev，项目名称:beast-mcmc，代码行数:4，代码来源:CodonPartitionedRobustCountingTest.java

注：本文中的dr.evolution.datatype.Codons.UNIVERSAL属性示例由纯净天空整理自Github/MSDocs等开源代码及文档管理平台，相关代码片段筛选自各路编程大神贡献的开源项目，源码版权归原作者所有，传播和使用请参考对应项目的License；未经允许，请勿转载。