本文整理汇总了Java中beast.evolution.tree.coalescent.ConstantPopulation类的典型用法代码示例。如果您正苦于以下问题：Java ConstantPopulation类的具体用法？Java ConstantPopulation怎么用？Java ConstantPopulation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。
ConstantPopulation类属于beast.evolution.tree.coalescent包，在下文中一共展示了ConstantPopulation类的14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.coalescent.ConstantPopulation; //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.coalescent.ConstantPopulation; //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.coalescent.ConstantPopulation; //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: init
import beast.evolution.tree.coalescent.ConstantPopulation; //导入依赖的package包/类
@Override
public void init(Input<?> input, BEASTInterface beastObject, int itemNr, ExpandOption isExpandOption,
boolean addButtons) {
ConstantPopulation population = (ConstantPopulation) input.get();
try {
InputEditor editor = doc.inputEditorFactory.createInputEditor(population.popSizeParameter, population, doc);
add(editor.getComponent());
} catch (NoSuchMethodException | SecurityException | ClassNotFoundException | InstantiationException
| IllegalAccessException | IllegalArgumentException | InvocationTargetException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
// TODO Auto-generated method stub
//super.init(input, beastObject, itemNr, isExpandOption, addButtons);
}
开发者ID:CompEvol，项目名称:beast2，代码行数:16，代码来源:ConstantPopulationInputEditor.java
示例5: testConstantPopulation
import beast.evolution.tree.coalescent.ConstantPopulation; //导入依赖的package包/类
public void testConstantPopulation() throws Exception {
// *********** 3 taxon **********
Tree tree = getTree(data, trees[0]);
TreeIntervals treeIntervals = new TreeIntervals();
treeIntervals.initByName("tree", tree);
ConstantPopulation cp = new ConstantPopulation();
cp.initByName("popSize", Double.toString(pop));
Coalescent coal = new Coalescent();
coal.initByName("treeIntervals", treeIntervals, "populationModel", cp);
double logL = coal.calculateLogP();
assertEquals(logL, -(4 / pop) - 2 * Math.log(pop), PRECISION);
// *********** 4 taxon **********
// tree = getTree(data, trees[1]);
// treeIntervals = new TreeIntervals();
// treeIntervals.initByName("tree", tree);
//
// cp = new ConstantPopulation();
// cp.initByName("popSize", Double.toString(pop));
//
// coal = new Coalescent();
// coal.initByName("treeIntervals", treeIntervals, "populationModel", cp);
//
// logL = coal.calculateLogP();
//
// assertEquals(logL, -(4 / pop) - 2 * Math.log(pop), PRECISION);
}
开发者ID:CompEvol，项目名称:beast2，代码行数:33，代码来源:CoalescentTest.java
示例6: getTree
import beast.evolution.tree.coalescent.ConstantPopulation; //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7: main
import beast.evolution.tree.coalescent.ConstantPopulation; //导入依赖的package包/类
public static void main(String[] args) throws Exception {
ConversionGraph acg = new ConversionGraph();
ConstantPopulation popFunc = new ConstantPopulation();
AddRemoveConversion operator = new AddRemoveConversion();
operator.initByName("weight", 1.0,
"acg", acg,
"populationModel", popFunc,
"rho", new RealParameter(Double.toString(1.0/10000.0)),
"delta", new RealParameter("50.0"));
popFunc.initByName("popSize", new RealParameter("1.0"));
TaxonSet taxonSet = new TaxonSet();
taxonSet.taxonsetInput.setValue(new Taxon("t1"), taxonSet);
taxonSet.taxonsetInput.setValue(new Taxon("t2"), taxonSet);
Locus locus = new Locus("locus", 10000);
try (PrintStream ps = new PrintStream("out.txt")) {
for (int i=0; i<100000; i++) {
acg.initByName(
"locus", locus,
"taxonset", taxonSet,
"fromString", "(0:1.0,1:1.0)2:0.0;");
operator.drawNewConversion();
ps.println(acg.getConversions(locus).get(0).getStartSite() + " "
+ acg.getConversions(locus).get(0).getEndSite());
}
}
}
开发者ID:tgvaughan，项目名称:bacter，代码行数:35，代码来源:AddRemoveConversion.java
示例8: getRandomTree
import beast.evolution.tree.coalescent.ConstantPopulation; //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9: getRandomTree
import beast.evolution.tree.coalescent.ConstantPopulation; //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
示例10: testMascotUnstructured
import beast.evolution.tree.coalescent.ConstantPopulation; //导入依赖的package包/类
@Test
public void testMascotUnstructured(){
//build alignment
Sequence sequence1 = new Sequence();
Sequence sequence2 = new Sequence();
Sequence sequence3 = new Sequence();
Sequence sequence4 = new Sequence();
Sequence sequence5 = new Sequence();
sequence1.initByName("taxon", "a1", "value", "???");
sequence2.initByName("taxon", "a2", "value", "???");
sequence3.initByName("taxon", "a3", "value", "???");
sequence4.initByName("taxon", "b1", "value", "???");
sequence5.initByName("taxon", "b2", "value", "???");
Alignment alignment = new Alignment();
alignment.initByName("sequence", sequence1,"sequence", sequence2,"sequence", sequence3,"sequence", sequence4, "sequence", sequence5);
TaxonSet taxa = new TaxonSet();
taxa.initByName("alignment", alignment);
//build trait set
TraitSet traitSet = new TraitSet();
traitSet.initByName("value", "a1=a,a2=a,a3=a,b1=a,b2=a", "traitname", "type", "taxa", taxa);
Tree tree = new TreeParser("(((a1:1,a2:2):1,(b1:1,b2:1.5):2):1,a3:1)");
Tree traitTree = new Tree();
tree.initByName("taxonset", taxa, "trait", traitSet);
StructuredTreeIntervals st = new StructuredTreeIntervals();
st.initByName("tree",tree);
// build constant dynamics
RealParameter Ne = new RealParameter("1.5 2");
RealParameter backwardsMigration = new RealParameter("0 0");
int dim = 2;
Constant constant = new Constant();
constant.initByName("backwardsMigration", backwardsMigration, "Ne", Ne, "dimension", dim, "typeTrait", traitSet);
Mascot mascot = new Mascot();
mascot.initByName("structuredTreeIntervals", st, "dynamics", constant);
// also set up the constant coalescent
TreeIntervals ti = new TreeIntervals();
ti.initByName("tree",tree);
RealParameter Nec = new RealParameter("1.5");
ConstantPopulation cp = new ConstantPopulation();
cp.initByName("popSize", Nec);
Coalescent coalescent = new Coalescent();
coalescent.initByName("populationModel", cp, "treeIntervals", ti);
Assert.assertTrue(Math.abs(mascot.calculateLogP()-coalescent.calculateLogP())<0.000000001);
}
开发者ID:nicfel，项目名称:Mascot，代码行数:61，代码来源:MascotTest.java
示例11: type
import beast.evolution.tree.coalescent.ConstantPopulation; //导入依赖的package包/类
@Override
public Class<?> type() {
return ConstantPopulation.class;
}
开发者ID:CompEvol，项目名称:beast2，代码行数:5，代码来源:ConstantPopulationInputEditor.java
示例12: testLikelihoodUsingSimulatedData
import beast.evolution.tree.coalescent.ConstantPopulation; //导入依赖的package包/类
@Test
public void testLikelihoodUsingSimulatedData() throws Exception {
ConstantPopulation popFunc = new ConstantPopulation();
popFunc.initByName("popSize", new RealParameter("1.0"));
Locus locus = new Locus("locus", 10000);
TaxonSet taxonSet = getTaxonSet(10);
ConversionGraph acg = new SimulatedACG();
acg.initByName(
"rho", 5.0/locus.getSiteCount(),
"delta", 1000.0,
"populationModel", popFunc,
"locus", locus,
"taxonset", taxonSet);
System.out.println(acg);
// Site model:
JukesCantor jc = new JukesCantor();
jc.initByName();
SiteModel siteModel = new SiteModel();
siteModel.initByName(
"mutationRate", new RealParameter("1"),
"substModel", jc);
// Simulate alignment:
SimulatedAlignment alignment = new SimulatedAlignment();
alignment.initByName(
"acg", acg,
"siteModel", siteModel,
"outputFileName", "simulated_alignment.nexus",
"useNexus", true);
// Calculate likelihood:
ACGLikelihood argLikelihood = new ACGLikelihood();
argLikelihood.initByName(
"locus", locus,
"data", alignment,
"tree", acg,
"siteModel", siteModel);
double logP = argLikelihood.calculateLogP();
// Compare product of likelihoods of "marginal alignments" with
// likelihood computed using RGL.
ACGLikelihoodSlow argLikelihoodSlow = new ACGLikelihoodSlow();
argLikelihoodSlow.initByName(
"locus", locus,
"data", alignment,
"tree", acg,
"siteModel", siteModel);
double logPprime = argLikelihoodSlow.calculateLogP();
double relError = 2.0*Math.abs(logP-logPprime)/Math.abs(logP + logPprime);
System.out.format("logP=%g\nlogPprime=%g\nrelError=%g\n",
logP, logPprime, relError);
assertTrue(relError<1e-13);
}
开发者ID:tgvaughan，项目名称:bacter，代码行数:63，代码来源:ACGLikelihoodTest.java
示例13: drawNewConversion
import beast.evolution.tree.coalescent.ConstantPopulation; //导入依赖的package包/类
/**
* Tests that probability density of forward move calculated
by drawNewConversion() matches probability density of backward
move calculated by getConversionProb().
*
* @throws Exception
*/
@Test
public void testHR() throws Exception {
ConstantPopulation popFunc = new ConstantPopulation();
popFunc.initByName("popSize", new RealParameter("1.0"));
Locus locus = new Locus("locus", 10000);
TaxonSet taxonSet = getTaxonSet(10);
SimulatedACG acg = new SimulatedACG();
acg.initByName(
"rho", 1.0/locus.getSiteCount(),
"delta", 50.0,
"locus", locus,
"taxonset", taxonSet,
"populationModel", popFunc);
AddRemoveConversion operator = new AddRemoveConversion();
// Loop until a valid proposal is made
double logP1;
List<Conversion> oldConversions;
do {
operator.initByName(
"weight", 1.0,
"acg", acg,
"delta", new RealParameter("50.0"),
"populationModel", popFunc);
oldConversions = Lists.newArrayList(
acg.getConversions(locus));
logP1 = operator.drawNewConversion();
} while (Double.isInfinite(logP1));
System.out.println("logP1 = " + logP1);
// Identify new recomination
Conversion newRecomb = null;
for (Conversion recomb : acg.getConversions(locus)) {
if (!oldConversions.contains(recomb))
newRecomb = recomb;
}
assertNotNull(newRecomb);
double logP2 = operator.getConversionProb(newRecomb);
System.out.println("logP2 = " + logP2);
assertTrue(Math.abs(logP1-logP2)<1e-10);
}
开发者ID:tgvaughan，项目名称:bacter，代码行数:59，代码来源:AddRemoveConversionTest.java
示例14: testProbability
import beast.evolution.tree.coalescent.ConstantPopulation; //导入依赖的package包/类
/**
* Tests whether probability of proposing a conversion lines up with
* conversion probability found in ACGCoalescent.
* @throws java.lang.Exception
*/
@Test
public void testProbability() throws Exception {
ConstantPopulation popFunc = new ConstantPopulation();
popFunc.initByName("popSize", new RealParameter("1.0"));
Locus locus = new Locus("locus", 10000);
TaxonSet taxonSet = getTaxonSet(10);
SimulatedACG acg = new SimulatedACG();
acg.initByName(
"rho", 1.0/locus.getSiteCount(),
"delta", 50.0,
"locus", locus,
"taxonset", taxonSet,
"populationModel", popFunc);
RealParameter rho = new RealParameter(Double.toString(1.0/locus.getSiteCount()));
RealParameter delta = new RealParameter("50.0");
AddRemoveConversion operator = new AddRemoveConversion();
operator.initByName(
"weight", 1.0,
"acg", acg,
"delta", delta,
"populationModel", popFunc);
ACGCoalescent coal = new ACGCoalescent();
coal.initByName(
"tree", acg,
"populationModel", popFunc,
"rho", rho,
"delta", delta);
double logP1 = 0.0;
double logP2 = 0.0;
for (Conversion conv : acg.getConversions(locus)) {
logP1 += operator.getConversionProb(conv);
logP2 += coal.calculateConversionLogP(conv);
}
System.out.println("logP1 = " + logP1);
System.out.println("logP2 = " + logP2);
assertTrue(Math.abs(logP1-logP2)<1e-10);
}
开发者ID:tgvaughan，项目名称:bacter，代码行数:54，代码来源:AddRemoveConversionTest.java
注：本文中的beast.evolution.tree.coalescent.ConstantPopulation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。 |
客服电话
APP下载
官方微信
请发表评论