本文整理汇总了Java中beast.evolution.branchratemodel.BranchRateModel.Base方法的典型用法代码示例。如果您正苦于以下问题:Java BranchRateModel.Base方法的具体用法?Java BranchRateModel.Base怎么用?Java BranchRateModel.Base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.branchratemodel.BranchRateModel
的用法示例。
在下文中一共展示了BranchRateModel.Base方法的11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; //导入方法依赖的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2: log
import beast.evolution.branchratemodel.BranchRateModel; //导入方法依赖的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3: NewWVTreeLikelihood
import beast.evolution.branchratemodel.BranchRateModel; //导入方法依赖的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4: log
import beast.evolution.branchratemodel.BranchRateModel; //导入方法依赖的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5: log
import beast.evolution.branchratemodel.BranchRateModel; //导入方法依赖的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6: TempSiteTreeLikelihood
import beast.evolution.branchratemodel.BranchRateModel; //导入方法依赖的package包/类
public TempSiteTreeLikelihood(Alignment data,
Tree tree,
boolean useAmbiguities,
SiteModel siteModel,
BranchRateModel.Base branchRateModel){
super(data,tree,useAmbiguities,siteModel,branchRateModel);
}
示例7: QuietTreeLikelihood
import beast.evolution.branchratemodel.BranchRateModel; //导入方法依赖的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8: TempWVTreeLikelihood
import beast.evolution.branchratemodel.BranchRateModel; //导入方法依赖的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9: SepTempTreeLikelihood
import beast.evolution.branchratemodel.BranchRateModel; //导入方法依赖的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10: setUpOperator
import beast.evolution.branchratemodel.BranchRateModel; //导入方法依赖的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();
}
}
示例11: toNewick
import beast.evolution.branchratemodel.BranchRateModel; //导入方法依赖的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();
}