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Java BranchRateModel类代码示例

原作者: [db:作者] 来自: [db:来源] 收藏 邀请

本文整理汇总了Java中beast.evolution.branchratemodel.BranchRateModel类的典型用法代码示例。如果您正苦于以下问题：Java BranchRateModel类的具体用法？Java BranchRateModel怎么用？Java BranchRateModel使用的例子？那么恭喜您, 这里精选的类代码示例或许可以为您提供帮助。



BranchRateModel类属于beast.evolution.branchratemodel包，在下文中一共展示了BranchRateModel类的20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，您的评价将有助于我们的系统推荐出更棒的Java代码示例。

示例1: log

import beast.evolution.branchratemodel.BranchRateModel; //导入依赖的package包/类
@Override
public void log(int nSample, PrintStream out) {
    // make sure we get the current version of the inputs
    SpeciesTreeInterface speciesTree = speciesTreeInput.get();
    SpeciesTreeInterface tree = (SpeciesTreeInterface) speciesTree.getCurrent();
    List<Function> metadata = parameterInput.get();
    for (int i = 0; i < metadata.size(); i++) {
        if (metadata.get(i) instanceof StateNode) {
            metadata.set(i, ((StateNode) metadata.get(i)).getCurrent());
        }
    }
    BranchRateModel branchRateModel = clockModelInput.get();
    PopulationModel populationModel = populationModelInput.get();
    // write out the log tree with meta data
    out.print("tree STATE_" + nSample + " = ");
    tree.getRoot().sort();
    out.print(toNewick(tree.getRoot(), metadata, branchRateModel, populationModel));
    //out.print(tree.getRoot().toShortNewick(false));
    out.print(";");
}
开发者ID:genomescale，项目名称:starbeast2，代码行数:21，代码来源:SpeciesTreeLogger.java


示例2: log

import beast.evolution.branchratemodel.BranchRateModel; //导入依赖的package包/类
@Override
public void log(int sample, PrintStream out) {
    // make sure we get the current version of the inputs
    Tree tree = (Tree) treeInput.get().getCurrent();
    List<Function> metadata = parameterInput.get();
    for (int i = 0; i < metadata.size(); i++) {
    	if (metadata.get(i) instanceof StateNode) {
    		metadata.set(i, ((StateNode) metadata.get(i)).getCurrent());
    	}
    }
    BranchRateModel.Base branchRateModel = clockModelInput.get();
    // write out the log tree with meta data
    out.print("tree STATE_" + sample + " = ");
    tree.getRoot().sort();
    out.print(toNewick(tree.getRoot(), metadata, branchRateModel));
    //out.print(tree.getRoot().toShortNewick(false));
    out.print(";");
}
开发者ID:CompEvol，项目名称:beast2，代码行数:19，代码来源:TreeWithMetaDataLogger.java


示例3: log

import beast.evolution.branchratemodel.BranchRateModel; //导入依赖的package包/类
@Override
public void log(int nSample, PrintStream out) {
	// make sure we get the current version of the inputs
       Tree tree = (Tree) treeInput.get().getCurrent();
       List<Function> metadata = parameterInput.get();
       for (int i = 0; i<metadata.size(); i++) {
           if (metadata.get(i) instanceof StateNode)
               metadata.set(i, ((StateNode) metadata.get(i)).getCurrent());
       }
       BranchRateModel.Base branchRateModel = clockModelInput.get();
       // write out the log tree with meta data
       out.print("tree STATE_" + nSample + " = ");
	tree.getRoot().sort();
       if(scaler != null){
           scaleFactor = scaler.getScaleFactor();
       }else{
           scaleFactor = scaleParameter.getValue();
       }
	out.print(toNewick(tree.getRoot(), metadata, branchRateModel, scaleFactor));
       //out.print(tree.getRoot().toShortNewick(false));
       out.print(";");
}
开发者ID:jessiewu，项目名称:substBMA，代码行数:23，代码来源:ScaledTreeWithMetaDataLogger.java


示例4: NewWVTreeLikelihood

import beast.evolution.branchratemodel.BranchRateModel; //导入依赖的package包/类
public NewWVTreeLikelihood(int[] patternWeights,
                           Alignment data,
                           Tree tree,
                           boolean useAmbiguities,
                           SiteModel siteModel,
                           BranchRateModel.Base branchRateModel){
    this.patternWeights = patternWeights;
    storedPatternWeights = new int[patternWeights.length];
    this.data = data;
    this.tree = tree;
    this.useAmbiguities = useAmbiguities;
    m_siteModel = siteModel;
    this.branchRateModel = branchRateModel;
    this.substitutionModel = (SubstitutionModel.Base)m_siteModel.getSubstitutionModel();
    setup();
}
开发者ID:jessiewu，项目名称:substBMA，代码行数:17，代码来源:NewWVTreeLikelihood.java


示例5: testSequenceSimulator

import beast.evolution.branchratemodel.BranchRateModel; //导入依赖的package包/类
public void testSequenceSimulator() throws Exception {
        Alignment dummyAlg = getDummyAlignment(taxa);
        SiteModel siteModel = getSiteModel(dummyAlg);
        BranchRateModel branchRateModel = getBranchModel(clockRate);

        SequenceSimulator sequenceSimulator = new SequenceSimulator(); // sequence length default 1000
        sequenceSimulator.initByName("data", dummyAlg, "tree", tree, "siteModel", siteModel,
                "branchRateModel", branchRateModel, "sequencelength", sequenceLength);

        Alignment simAlg = sequenceSimulator.simulate();

        for (Sequence seq : simAlg.sequenceInput.get()) {
            System.out.println(">" + seq.taxonInput.get());
            System.out.println(seq.dataInput.get());
        }

//        ClusterTree upgma = new ClusterTree();
//        upgma.initByName("clusterType", "upgma", "taxa", simAlg,
////                "distance", , // default Jukes Cantor
//                "clock.rate", Double.toString(clockRate));
//        System.out.println(upgma.getRoot().toNewick(false));
    }
开发者ID:CompEvol，项目名称:NZGOT，代码行数:23，代码来源:SequenceSimulatorTest.java


示例6: log

import beast.evolution.branchratemodel.BranchRateModel; //导入依赖的package包/类
@Override
    public void log(int nSample, PrintStream out) {
    	states = mascotInput.get().dynamicsInput.get().getDimension();
    	
        // make sure we get the current version of the inputs
//        Tree tree = (Tree) mascotInput.get().treeIntervalsInput.get().treeInput.get().getCurrent();
        //calculate the state of each node
    	calculateNodeStates();
    	
    	used = new boolean[stateProbabilities.length];
    	report = false;
        List<Function> metadata = parameterInput.get();
        for (int i = 0; i < metadata.size(); i++) {
        	if (metadata.get(i) instanceof StateNode) {
        		metadata.set(i, ((StateNode) metadata.get(i)).getCurrent());
        	}
        }
        BranchRateModel.Base branchRateModel = clockModelInput.get();
        // write out the log tree with meta data
        out.print("tree STATE_" + nSample + " = ");
        mascotInput.get().treeIntervalsInput.get().treeInput.get().getRoot().sort();
        root = mascotInput.get().treeIntervalsInput.get().treeInput.get().getRoot();
        out.print(toNewick(root, metadata, branchRateModel));
        out.print(";");
        
        for (int i = 0; i < used.length; i++)
        	if(!used[i])
        		System.err.println("not all nodes used");
        if (report)
        	System.err.println("error in node numbers");
    }
开发者ID:nicfel，项目名称:Mascot，代码行数:32，代码来源:StructuredTreeLoggerCollaps.java


示例7: log

import beast.evolution.branchratemodel.BranchRateModel; //导入依赖的package包/类
@Override
    public void log(int nSample, PrintStream out) {
    	states = mascotInput.get().dynamicsInput.get().getDimension();
    	
        // make sure we get the current version of the inputs
//        Tree tree = (Tree) mascotInput.get().treeIntervalsInput.get().treeInput.get().getCurrent();
        //calculate the state of each node
    	try {
			CalculateNodeStates();
		} catch (Exception e) {
			// TODO Auto-generated catch block
			e.printStackTrace();
		}
    	
    	used = new boolean[stateProbabilities.length];
    	report = false;
        List<Function> metadata = parameterInput.get();
        for (int i = 0; i < metadata.size(); i++) {
        	if (metadata.get(i) instanceof StateNode) {
        		metadata.set(i, ((StateNode) metadata.get(i)).getCurrent());
        	}
        }
        BranchRateModel.Base branchRateModel = clockModelInput.get();
        // write out the log tree with meta data
        out.print("tree STATE_" + nSample + " = ");
        mascotInput.get().treeIntervalsInput.get().treeInput.get().getRoot().sort();
        root = mascotInput.get().treeIntervalsInput.get().treeInput.get().getRoot();
        out.print(toNewick(root, metadata, branchRateModel));
        out.print(";");
        
        for (int i = 0; i < used.length; i++)
        	if(!used[i])
        		System.err.println("not all nodes used");
        if (report)
        	System.err.println("error in node numbers");
    }
开发者ID:nicfel，项目名称:Mascot，代码行数:37，代码来源:StructuredTreeLogger.java


示例8: getClockModel

import beast.evolution.branchratemodel.BranchRateModel; //导入依赖的package包/类
BranchRateModel getClockModel(String partition) {
    int k = 0;
    for (Alignment data : alignments) {
        if (data.getID().equals(partition)) {
            return clockModels.get(k);
        }
        k++;
    }
    return null;
}
开发者ID:CompEvol，项目名称:beast2，代码行数:11，代码来源:BeautiDoc.java


示例9: TempSiteTreeLikelihood

import beast.evolution.branchratemodel.BranchRateModel; //导入依赖的package包/类
public TempSiteTreeLikelihood(Alignment data,
                           Tree tree,
                           boolean useAmbiguities,
                           SiteModel siteModel,
                           BranchRateModel.Base branchRateModel){
    super(data,tree,useAmbiguities,siteModel,branchRateModel);

}
开发者ID:jessiewu，项目名称:substBMA，代码行数:9，代码来源:TempSiteTreeLikelihood.java


示例10: QuietTreeLikelihood

import beast.evolution.branchratemodel.BranchRateModel; //导入依赖的package包/类
public QuietTreeLikelihood(Alignment data,
                           Tree tree,
                           boolean useAmbiguities,
                           SiteModel siteModel,
                           BranchRateModel.Base branchRateModel){
    this.data = data;
    this.tree = tree;
    this.useAmbiguities = useAmbiguities;
    m_siteModel = siteModel;
    this.branchRateModel = branchRateModel;
    substitutionModel = m_siteModel.getSubstitutionModel();
    setup();

}
开发者ID:jessiewu，项目名称:substBMA，代码行数:15，代码来源:QuietTreeLikelihood.java


示例11: TempWVTreeLikelihood

import beast.evolution.branchratemodel.BranchRateModel; //导入依赖的package包/类
public TempWVTreeLikelihood(int[] patternWeights,
                           Alignment data,
                           Tree tree,
                           boolean useAmbiguities,
                           SiteModel siteModel,
                           BranchRateModel.Base branchRateModel){
    super(patternWeights, data, tree, useAmbiguities, siteModel, branchRateModel);
}
开发者ID:jessiewu，项目名称:substBMA，代码行数:9，代码来源:TempWVTreeLikelihood.java


示例12: SepTempTreeLikelihood

import beast.evolution.branchratemodel.BranchRateModel; //导入依赖的package包/类
public SepTempTreeLikelihood(Alignment alignment,
                          Tree tree,
                          boolean useAmbiguities,
                          SiteModel siteModel,
                          BranchRateModel.Base branchRateModel,
                          DPNtdRateSepSiteModel dpNtdRateSepSiteModel){
    super(alignment, tree, useAmbiguities, siteModel, branchRateModel);
    this.dpNtdRateSepSiteModel = dpNtdRateSepSiteModel;

}
开发者ID:jessiewu，项目名称:substBMA，代码行数:11，代码来源:SepTempTreeLikelihood.java


示例13: getSimulatedAlignment

import beast.evolution.branchratemodel.BranchRateModel; //导入依赖的package包/类
public Alignment getSimulatedAlignment(Alignment dummyAlg, Tree tree, SiteModel siteModel, BranchRateModel branchRateModel) throws Exception {
    // feed to sequence simulator and generate leaves
    SequenceSimulator sequenceSimulator = new SequenceSimulator(); // sequence length default 1000
    sequenceSimulator.init(dummyAlg, tree, siteModel, branchRateModel);

    return sequenceSimulator.simulate();
}
开发者ID:CompEvol，项目名称:NZGOT，代码行数:8，代码来源:TreeSeqSimulatorCustomized.java


示例14: getSimulatedAlignment

import beast.evolution.branchratemodel.BranchRateModel; //导入依赖的package包/类
public Alignment getSimulatedAlignment(Alignment dummyAlg, Tree tree, SiteModel siteModel,
                                       BranchRateModel branchRateModel, int sequenceLength) throws Exception {
    // feed to sequence simulator and generate leaves
    SequenceSimulator sequenceSimulator = new SequenceSimulator(); // sequence length default 1000
    sequenceSimulator.initByName("data", dummyAlg, "tree", tree, "siteModel", siteModel,
            "branchRateModel", branchRateModel, "sequencelength", sequenceLength);

    return sequenceSimulator.simulate();
}
开发者ID:CompEvol，项目名称:NZGOT，代码行数:10，代码来源:TreeSeqSimulator.java


示例15: main

import beast.evolution.branchratemodel.BranchRateModel; //导入依赖的package包/类
@SuppressWarnings("unchecked")
public static void main(String[] args) {
    try {
        // parse arguments
        if (args.length < 2) {
            printUsageAndExit();
        }
        String fileName = args[0];
        int replications = Integer.parseInt(args[1]);
        PrintStream out = System.out;
        if (args.length == 3) {
            File file = new File(args[2]);
            out = new PrintStream(file);
        }

        // grab the file
        String xml = "";
        BufferedReader fin = new BufferedReader(new FileReader(fileName));
        while (fin.ready()) {
            xml += fin.readLine();
        }
        fin.close();

        // parse the xml
        XMLParser parser = new XMLParser();
        BEASTInterface beastObject = parser.parseFragment(xml, true);

        // find relevant objects from the model
        TreeLikelihood treeLikelihood = getTreeLikelihood(beastObject);
        if (treeLikelihood == null) {
            throw new IllegalArgumentException("No treelikelihood found in file. Giving up now.");
        }
        Alignment data = ((Input<Alignment>) treeLikelihood.getInput("data")).get();
        Tree tree = ((Input<Tree>) treeLikelihood.getInput("tree")).get();
        SiteModel pSiteModel = ((Input<SiteModel>) treeLikelihood.getInput("siteModel")).get();
        BranchRateModel pBranchRateModel = ((Input<BranchRateModel>) treeLikelihood.getInput("branchRateModel")).get();


        // feed to sequence simulator and generate leaves
        SequenceSimulator treeSimulator = new SequenceSimulator();
        treeSimulator.init(data, tree, pSiteModel, pBranchRateModel, replications);
        XMLProducer producer = new XMLProducer();
        Alignment alignment = treeSimulator.simulate();
        xml = producer.toRawXML(alignment);
        out.println("<beast version='2.0'>");
        out.println(xml);
        out.println("</beast>");
    } catch (Exception e) {
        e.printStackTrace();
    }
}
开发者ID:CompEvol，项目名称:beast2，代码行数:52，代码来源:SequenceSimulator.java


示例16: setUpOperator

import beast.evolution.branchratemodel.BranchRateModel; //导入依赖的package包/类
/** set up relative weights and parameter input **/
   private void setUpOperator() {
   	String weights = "";
   	List<RealParameter> parameters = operator.parameterInput.get();
   	parameters.clear();
   	double commonClockRate = -1;
   	boolean isAllClocksAreEqual = true;
	try {
    	for (int i = 0; i < doc.alignments.size(); i++) {
    		Alignment data = doc.alignments.get(i); 
    		int weight = data.getSiteCount();
    		BranchRateModel.Base clockModel = (BranchRateModel.Base) doc.clockModels.get(i);
    		RealParameter clockRate = clockModel.meanRateInput.get();
    		//clockRate.m_bIsEstimated.setValue(true, clockRate);
    		if (clockRate.isEstimatedInput.get()) {
    			if (commonClockRate < 0) {
    				commonClockRate = clockRate.valuesInput.get().get(0);
    			} else {
    				if (Math.abs(commonClockRate - clockRate.valuesInput.get().get(0)) > 1e-10) {
    					isAllClocksAreEqual = false;
    				}
    			}
   				weights += weight + " ";
    			parameters.add(clockRate);
    		}
    		//doc.autoSetClockRate = false;
    	}
    	if (!fixMeanRatesCheckBox.isSelected()) {
    		fixMeanRatesValidateLabel.setVisible(false);
    		return;
    	}
    	if (parameters.size() == 0) {
    		fixMeanRatesValidateLabel.setVisible(true);
    		fixMeanRatesValidateLabel.m_circleColor = Color.red;
    		fixMeanRatesValidateLabel.setToolTipText("The model is invalid: At least one clock rate should be estimated.");
    		return;
    	}

    	IntegerParameter weightParameter = new IntegerParameter(weights);
		weightParameter.setID("weightparameter");
		weightParameter.isEstimatedInput.setValue(false, weightParameter);
    	operator.parameterWeightsInput.setValue(weightParameter, operator);
    	if (!isAllClocksAreEqual) {
    		fixMeanRatesValidateLabel.setVisible(true);
    		fixMeanRatesValidateLabel.m_circleColor = Color.orange;
    		fixMeanRatesValidateLabel.setToolTipText("Not all clocks are equal. Are you sure this is what you want?");
    	} else if (parameters.size() == 1) {
    		fixMeanRatesValidateLabel.setVisible(true);
    		fixMeanRatesValidateLabel.m_circleColor = Color.orange;
    		fixMeanRatesValidateLabel.setToolTipText("At least 2 clock models should have their rate estimated");
    	} else if (parameters.size() < doc.alignments.size()) {
    		fixMeanRatesValidateLabel.setVisible(true);
    		fixMeanRatesValidateLabel.m_circleColor = Color.orange;
    		fixMeanRatesValidateLabel.setToolTipText("Not all partitions have their rate estimated");
    	} else {
    		fixMeanRatesValidateLabel.setVisible(false);
    	}
		repaint();
   		//doc.autoSetClockRate = true;
	} catch (Exception e) {
		// TODO Auto-generated catch block
		e.printStackTrace();
	}
}
开发者ID:CompEvol，项目名称:beast2，代码行数:65，代码来源:ClockModelListInputEditor.java


示例17: toNewick

import beast.evolution.branchratemodel.BranchRateModel; //导入依赖的package包/类
String toNewick(Node node, List<Function> metadataList, BranchRateModel.Base branchRateModel, double scaleFactor) {
    StringBuffer buf = new StringBuffer();
    if (node.getLeft() != null) {
        buf.append("(");
        buf.append(toNewick(node.getLeft(), metadataList, branchRateModel, scaleFactor));
        if (node.getRight() != null) {
            buf.append(',');
            buf.append(toNewick(node.getRight(), metadataList, branchRateModel, scaleFactor));
        }
        buf.append(")");
    } else {
        buf.append(node.labelNr + 1);
    }

    if (someMetaDataNeedsLogging) {
        buf.append("[&");
        if (metadataList.size() > 0) {
            for (Function metadata : metadataList) {
                buf.append(((BEASTObject)metadata).getID());
                buf.append('=');
                if (metadata instanceof Parameter<?>) {
                    Parameter<?> p = (Parameter<?>) metadata;
                    int dim = p.getMinorDimension1();
                    if (dim > 1) {
                        buf.append('{');
                        for (int i = 0; i < dim; i++) {
                            buf.append(p.getMatrixValue(node.labelNr, i));
                            if (i < dim - 1) {
                                buf.append(',');
                            }
                        }
                        buf.append('}');
                    } else {
                        buf.append(metadata.getArrayValue(node.labelNr));
                    }
                } else {
                    buf.append(metadata.getArrayValue(node.labelNr));
                }
                if (metadataList.indexOf(metadata) < metadataList.size() - 1) {
                    buf.append(",");
                }
            }
            if (branchRateModel != null) {
                buf.append(",");
            }
        }
        if (branchRateModel != null) {
            buf.append("rate=");
            appendDouble(buf, branchRateModel.getRateForBranch(node));
        }
        buf.append(']');
    }
    buf.append(":");
    if (substitutions) {
        appendDouble(buf, node.getLength() * branchRateModel.getRateForBranch(node));
    } else {
        appendDouble(buf, node.getLength());
    }
    return buf.toString();
}
开发者ID:jessiewu，项目名称:substBMA，代码行数:61，代码来源:ScaledTreeWithMetaDataLogger.java


示例18: getBranchModel

import beast.evolution.branchratemodel.BranchRateModel; //导入依赖的package包/类
public BranchRateModel getBranchModel(double clockRate) throws Exception {
    StrictClockModel strictClockModel = new StrictClockModel();
    strictClockModel.initByName("clock.rate", Double.toString(clockRate));

    return strictClockModel;
}
开发者ID:CompEvol，项目名称:NZGOT，代码行数:7，代码来源:TreeSeqSimulatorCustomized.java


示例19: getBranchModel

import beast.evolution.branchratemodel.BranchRateModel; //导入依赖的package包/类
protected BranchRateModel getBranchModel(double clockRate) throws Exception {
    StrictClockModel strictClockModel = new StrictClockModel();
    strictClockModel.initByName("clock.rate", Double.toString(clockRate));

    return strictClockModel;
}
开发者ID:CompEvol，项目名称:NZGOT，代码行数:7，代码来源:SequenceSimulatorTest.java


示例20: toNewick

import beast.evolution.branchratemodel.BranchRateModel; //导入依赖的package包/类
String toNewick(Node node, List<Function> metadataList, BranchRateModel branchRateModel, PopulationModel populationModel) {
    StringBuffer buf = new StringBuffer();
    if (node.getLeft() != null) {
        buf.append("(");
        buf.append(toNewick(node.getLeft(), metadataList, branchRateModel, populationModel));
        if (node.getRight() != null) {
            buf.append(',');
            buf.append(toNewick(node.getRight(), metadataList, branchRateModel, populationModel));
        }
        buf.append(")");
    } else {
        buf.append(node.getNr() + 1);
    }
    if (someMetaDataNeedsLogging) {
        buf.append("[&");
        if (metadataList.size() > 0) {
            for (Function metadata : metadataList) {
                buf.append(((BEASTObject)metadata).getID());
                buf.append('=');
                if (metadata instanceof Parameter<?>) {
                    Parameter<?> p = (Parameter<?>) metadata;
                    int dim = p.getMinorDimension1();
                    if (dim > 1) {
                        buf.append('{');
                        for (int i = 0; i < dim; i++) {
                            buf.append(p.getMatrixValue(node.getNr(), i));
                            if (i < dim - 1) {
                                buf.append(',');
                            }
                        }
                        buf.append('}');
                    } else {
                        buf.append(metadata.getArrayValue(node.getNr()));
                    }
                } else {
                    buf.append(metadata.getArrayValue(node.getNr()));
                }
                if (metadataList.indexOf(metadata) < metadataList.size() - 1) {
                    buf.append(",");
                }
            }
            if (branchRateModel != null || populationModel != null) {
                buf.append(",");
            }
        }
        if (branchRateModel != null) {
            buf.append("rate=");
            appendDouble(buf, branchRateModel.getRateForBranch(node));
            if (populationModel != null) {
                buf.append(",");
            }
        }

        if (populationModel != null) {
            populationModel.serialize(node, buf, df);
        }

        buf.append(']');
    }
    buf.append(":");

    double nodeLength;
    if (node.isRoot()) {
        nodeLength = getTreeHeight() - node.getHeight();
    } else {
        nodeLength = node.getLength();
    }

    if (substitutions) {
        appendDouble(buf, nodeLength * branchRateModel.getRateForBranch(node));
    } else {
        appendDouble(buf, nodeLength);
    }
    return buf.toString();
}
开发者ID:genomescale，项目名称:starbeast2，代码行数:76，代码来源:SpeciesTreeLogger.java



注：本文中的beast.evolution.branchratemodel.BranchRateModel类示例整理自Github/MSDocs等源码及文档管理平台，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。

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