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: 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(";");
}
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(";");
}
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(";");
}
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();
}
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));
}
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");
}
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");
}
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;
}
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);
}
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();
}
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);
}
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;
}
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();
}
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();
}
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();
}
}