本文整理汇总了Java中beast.evolution.tree.RandomTree.initByName方法的典型用法代码示例。如果您正苦于以下问题：Java RandomTree.initByName方法的具体用法？Java RandomTree.initByName怎么用？Java RandomTree.initByName使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类beast.evolution.tree.RandomTree的用法示例。
在下文中一共展示了RandomTree.initByName方法的3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: randomTreeTest
import beast.evolution.tree.RandomTree; //导入方法依赖的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()));
}
示例2: getRandomTree
import beast.evolution.tree.RandomTree; //导入方法依赖的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;
}
示例3: getRandomTree
import beast.evolution.tree.RandomTree; //导入方法依赖的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;
}