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Java Codons.CILIATE属性代码示例

本文整理汇总了Java中dr.evolution.datatype.Codons.CILIATE属性的典型用法代码示例。如果您正苦于以下问题：Java Codons.CILIATE属性的具体用法？Java Codons.CILIATE怎么用？Java Codons.CILIATE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.CILIATE属性的5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: 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2: 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3: 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);
            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 = null;
        Parameter mntParam = null;
        if(xo.hasChildNamed(KAPPATSTV)) {
        	kappaParam = (Parameter)xo.getElementFirstChild(KAPPATSTV);
        	if(kappaParam.getDimension() != 2 && kappaParam.getDimension() != 9) {
            	throw new XMLParseException("If you use the kappa parameter, you need to enter exactly\n" +
            			"two values for ts and tv or nine values\n" +
            			"according to the Kosiol ECM+F+omega+9k model");
            }
    	} else {
    		mntParam = (Parameter)xo.getElementFirstChild(MULTI_NT_CHANGE);
    	}
    	
        String dirString = xo.getStringAttribute(ECM_DATA_DIR);
        String freqString = xo.getStringAttribute(ECM_FREQ_MATRIX);
        String matString = xo.getStringAttribute(ECM_DATA_MATRIX);
        
        EmpiricalRateMatrix rateMat = new EmpiricalRateMatrix(EMPIRICAL_RATE_MATRIX, codons, 
        													dirString, freqString, matString);

        FrequencyModel freqModel = null;
        if (xo.getChild(FrequencyModel.class) != null) {
        	freqModel = (FrequencyModel)xo.getChild(FrequencyModel.class);
        } else {
        	freqModel = createNewFreqModel(codons, rateMat);
        }

        return new EmpiricalCodonModel(codons, omegaParam, kappaParam, mntParam, rateMat, freqModel);
    }
开发者ID:whdc，项目名称:ieo-beast，代码行数:66，代码来源:EmpiricalCodonModelParser.java

示例5: 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 = null;
        Parameter mntParam = null;
        if(xo.hasChildNamed(KAPPATSTV)) {
        	kappaParam = (Parameter)xo.getElementFirstChild(KAPPATSTV);
        	if(kappaParam.getDimension() != 2 && kappaParam.getDimension() != 9) {
            	throw new XMLParseException("If you use the kappa parameter, you need to enter exactly\n" +
            			"two values for ts and tv or nine values\n" +
            			"according to the Kosiol ECM+F+omega+9k model");
            }
    	} else {
    		mntParam = (Parameter)xo.getElementFirstChild(MULTI_NT_CHANGE);
    	}
        
        String dirString = xo.getStringAttribute(ECM_DATA_DIR);
        String freqString = xo.getStringAttribute(ECM_FREQ_MATRIX);
        String matString = xo.getStringAttribute(ECM_DATA_MATRIX);
        
        EmpiricalCodonRateMatrix rateMat = new EmpiricalCodonRateMatrix(EMPIRICAL_RATE_MATRIX, codons, 
        													dirString, freqString, matString);

        // get frequencies from XML, from frequency csv file or estimate from data
        FrequencyModel freqModel = null;
        if (xo.getChild(FrequencyModel.class) != null) {
        	freqModel = (FrequencyModel)xo.getChild(FrequencyModel.class);
        } else {
        	freqModel = createNewFreqModel(codons, rateMat);
        }

        return new EmpiricalCodonModel(codons, omegaParam, kappaParam, mntParam, rateMat, freqModel);
    }
开发者ID:whdc，项目名称:ieo-beast，代码行数:67，代码来源:EmpiricalCodonModelParser.java


注：本文中的dr.evolution.datatype.Codons.CILIATE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。