本文整理汇总了Java中beast.evolution.tree.RandomTree类的典型用法代码示例。如果您正苦于以下问题：Java RandomTree类的具体用法？Java RandomTree怎么用？Java RandomTree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。
RandomTree类属于beast.evolution.tree包，在下文中一共展示了RandomTree类的6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: randomTreeTest
import beast.evolution.tree.RandomTree; //导入依赖的package包/类
private static void randomTreeTest() throws Exception {
StringBuilder traitSB = new StringBuilder();
List<Sequence> seqList = new ArrayList<Sequence>();
for (int i = 0; i < 10; i++) {
String taxonID = "t " + i;
seqList.add(new Sequence(taxonID, "?"));
if (i > 0)
traitSB.append(",");
traitSB.append(taxonID).append("=").append(i);
}
Alignment alignment = new Alignment(seqList, "nucleotide");
ConstantPopulation popFunc = new ConstantPopulation();
popFunc.initByName("popSize", new RealParameter("1.0"));
RandomTree t = new RandomTree();
t.initByName("taxa", alignment, "populationModel", popFunc);
Sequence l = new Sequence("", "");
System.out.println("Tree GTR Borrowing Test");
Tree tree = randomYuleTree(2, 0.01);
tree.getRoot().setMetaData("lang", l);
System.out.println(TreeUtils.getTreeLength(tree, tree.getRoot()));
}
开发者ID:lutrasdebtra，项目名称:Beast-Borrowing-Plugin，代码行数:27，代码来源:BeastBorrowingPluginTest.java
示例2: initWithMRCACalibrations
import beast.evolution.tree.RandomTree; //导入依赖的package包/类
private void initWithMRCACalibrations(List<MRCAPrior> calibrations) {
final Tree spTree = speciesTreeInput.get();
final RandomTree rnd = new RandomTree();
rnd.setInputValue("taxonset", spTree.getTaxonset());
for( final MRCAPrior cal : calibrations ) {
rnd.setInputValue("constraint", cal);
}
ConstantPopulation pf = new ConstantPopulation();
pf.setInputValue("popSize", new RealParameter("1.0"));
rnd.setInputValue("populationModel", pf);
rnd.initAndValidate();
spTree.assignFromWithoutID((Tree)rnd);
final double rootHeight = spTree.getRoot().getHeight();
randomInitGeneTrees(rootHeight);
}
开发者ID:CompEvol，项目名称:beast2，代码行数:19，代码来源:StarBeastStartState.java
示例3: randomInit
import beast.evolution.tree.RandomTree; //导入依赖的package包/类
private void randomInit(final SpeciesTree speciesTree, List<MRCAPrior> calibrations) {
final RealParameter birthRateParameter = birthRate.get();
final Double lambda = (birthRateParameter == null) ? 1.0 : birthRateParameter.getValue();
final Double initialPopSize = 1.0 / lambda; // scales coalescent tree height inverse to birth rate
final RealParameter popSize = new RealParameter(initialPopSize.toString());
final ConstantPopulation pf = new ConstantPopulation();
pf.setInputValue("popSize", popSize);
final RandomTree rnd = new RandomTree();
rnd.setInputValue("taxonset", speciesTree.getTaxonset());
if (speciesTree.hasDateTrait()) rnd.setInputValue("trait", speciesTree.getDateTrait());
for (final MRCAPrior cal: calibrations) rnd.setInputValue("constraint", cal);
rnd.setInputValue("populationModel", pf);
rnd.setInputValue("populationModel", pf);
rnd.initAndValidate();
speciesTree.assignFromWithoutID(rnd);
// System.out.println("BEFORE = " + speciesTree.toString());
/*final TraitSet speciesTipDates = speciesTree.getDateTrait();
if (speciesTree.hasDateTrait()) {
for (Node node: speciesTree.getNodesAsArray()) {
if (node.isLeaf()) {
final String taxonName = node.getID();
final double taxonHeight = speciesTipDates.getValue(taxonName);
node.setHeight(taxonHeight);
}
}
System.out.println("AFTER = " + speciesTree.toString());
}*/
}
开发者ID:genomescale，项目名称:starbeast2，代码行数:35，代码来源:StarBeastInitializer.java
示例4: getTree
import beast.evolution.tree.RandomTree; //导入依赖的package包/类
static public Tree getTree(TaxonSet taxa) throws Exception {
Tree tree = new RandomTree();
TraitSet dates = getDates(taxa);
ConstantPopulation constant = new ConstantPopulation();
constant.initByName("popSize", new RealParameter("5.0"));
tree.initByName(
"taxonset", taxa,
"populationModel", constant,
"trait", dates);
return tree;
}
开发者ID:CompEvol，项目名称:beast2，代码行数:12，代码来源:UnorderedAlignmentsTest.java
示例5: getRandomTree
import beast.evolution.tree.RandomTree; //导入依赖的package包/类
public Tree getRandomTree(double popSize, Alignment dummyAlg, String[] taxa, int[] dates) throws Exception {
TaxonSet taxonSet = new TaxonSet(dummyAlg);
StringBuilder traitSB = new StringBuilder();
for (int i=0; i<taxa.length; i++) {
if (i>0)
traitSB.append(",");
traitSB.append(taxa[i]).append("=").append(dates[i]);
}
// out.println(traitSB.toString());
TraitSet timeTrait = new TraitSet();
timeTrait.initByName(
"traitname", "date-backward",
"taxa", taxonSet,
"value", traitSB.toString());
ConstantPopulation popFunc = new ConstantPopulation();
popFunc.initByName("popSize", new RealParameter(Double.toString(popSize)));
// Create RandomTree and TreeInterval instances
RandomTree tree = new RandomTree();
// TreeIntervals intervals = new TreeIntervals();
tree.initByName(
"taxa", dummyAlg,
"populationModel", popFunc,
"trait", timeTrait);
// intervals.initByName("tree", tree);
return tree;
}
开发者ID:CompEvol，项目名称:NZGOT，代码行数:33，代码来源:TreeSeqSimulatorCustomized.java
示例6: getRandomTree
import beast.evolution.tree.RandomTree; //导入依赖的package包/类
public Tree getRandomTree(double popSize, Alignment dummyAlg, String[] taxa, int[] dates) throws Exception {
TaxonSet taxonSet = new TaxonSet(dummyAlg);
traitSB = new StringBuilder();
for (int i=0; i<taxa.length; i++) {
if (i>0)
traitSB.append(",");
traitSB.append(taxa[i]).append("=").append(dates[i]);
}
// out.println(traitSB.toString());
TraitSet timeTrait = new TraitSet();
timeTrait.initByName(
"traitname", traitName,
"taxa", taxonSet,
"value", traitSB.toString());
ConstantPopulation popFunc = new ConstantPopulation();
popFunc.initByName("popSize", new RealParameter(Double.toString(popSize)));
// Create RandomTree and TreeInterval instances
RandomTree tree = new RandomTree();
// TreeIntervals intervals = new TreeIntervals();
tree.initByName(
"taxa", dummyAlg,
"populationModel", popFunc,
"trait", timeTrait);
// intervals.initByName("tree", tree);
return tree;
}
开发者ID:CompEvol，项目名称:NZGOT，代码行数:33，代码来源:TreeSeqSimulator.java
注：本文中的beast.evolution.tree.RandomTree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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