Examples with GenericTreeLikelihood beast.evolution.likelihood.GenericTreeLikelihood used on opensource projects

Example 11 with GenericTreeLikelihood

use of beast.evolution.likelihood.GenericTreeLikelihood in project beast2 by CompEvol.

the class BeautiDoc method collectClockModels.

private void collectClockModels() {
    // collect branch rate models from model
    CompoundDistribution likelihood = (CompoundDistribution) pluginmap.get("likelihood");
    while (clockModels.size() < partitionNames.size()) {
        try {
            GenericTreeLikelihood treelikelihood = new GenericTreeLikelihood();
            treelikelihood.branchRateModelInput.setValue(new StrictClockModel(), treelikelihood);
            List<BeautiSubTemplate> availableBEASTObjects = inputEditorFactory.getAvailableTemplates(treelikelihood.branchRateModelInput, treelikelihood, null, this);
            BEASTInterface beastObject = availableBEASTObjects.get(0).createSubNet(partitionNames.get(clockModels.size()), true);
            clockModels.add((BranchRateModel.Base) beastObject);
        } catch (Exception e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }
    }
    int k = 0;
    for (Distribution d : likelihood.pDistributions.get()) {
        BranchRateModel clockModel = ((GenericTreeLikelihood) d).branchRateModelInput.get();
        // sanity check
        Tree tree = null;
        try {
            for (Input<?> input : ((BEASTInterface) clockModel).listInputs()) {
                if (input.getName().equals("tree")) {
                    tree = (Tree) input.get();
                }
            }
            if (tree != null && tree != ((GenericTreeLikelihood) d).treeInput.get()) {
                clockModel = clockModels.get(k);
                Log.warning.println("WARNING: unlinking clock model for " + d.getID());
                // TODO #557: this should move to the event of clock model drop box
                // JOptionPane.showMessageDialog(beauti.getSelectedComponent(),
                // "Cannot link all clock model(s) except strict clock with different trees !");
                ((GenericTreeLikelihood) d).branchRateModelInput.setValue(clockModel, d);
            }
        } catch (Exception e) {
        // ignore
        }
        if (clockModel != null) {
            String id = ((BEASTInterface) clockModel).getID();
            id = parsePartition(id);
            String partition = alignments.get(k).getID();
            if (id.equals(partition)) {
                clockModels.set(k, clockModel);
            }
            k++;
        }
    }
}

Example 12 with GenericTreeLikelihood

use of beast.evolution.likelihood.GenericTreeLikelihood in project beast2 by CompEvol.

the class SiteModelInputEditor method setUpOperator.

/**
 * set up relative weights and parameter input *
 */
public void setUpOperator() {
    boolean isAllClocksAreEqual = true;
    try {
        boolean hasOneEstimatedRate = customConnector(doc);
        if (doc.autoUpdateFixMeanSubstRate) {
            fixMeanRatesCheckBox.setSelected(hasOneEstimatedRate);
            doFixMeanRates(hasOneEstimatedRate);
        }
        try {
            double commonClockRate = -1;
            CompoundDistribution likelihood = (CompoundDistribution) doc.pluginmap.get("likelihood");
            for (Distribution d : likelihood.pDistributions.get()) {
                GenericTreeLikelihood treelikelihood = (GenericTreeLikelihood) d;
                if (treelikelihood.siteModelInput.get() instanceof SiteModel) {
                    SiteModel siteModel = (SiteModel) treelikelihood.siteModelInput.get();
                    RealParameter mutationRate = siteModel.muParameterInput.get();
                    // clockRate.m_bIsEstimated.setValue(true, clockRate);
                    if (mutationRate.isEstimatedInput.get()) {
                        if (commonClockRate < 0) {
                            commonClockRate = mutationRate.valuesInput.get().get(0);
                        } else {
                            if (Math.abs(commonClockRate - mutationRate.valuesInput.get().get(0)) > 1e-10) {
                                isAllClocksAreEqual = false;
                            }
                        }
                    }
                }
            }
        } catch (Exception e) {
        }
        List<RealParameter> parameters = operator.parameterInput.get();
        if (!fixMeanRatesCheckBox.isSelected()) {
            fixMeanRatesValidateLabel.setVisible(false);
            repaint();
            return;
        }
        if (parameters.size() == 0) {
            fixMeanRatesValidateLabel.setVisible(true);
            fixMeanRatesValidateLabel.m_circleColor = Color.red;
            fixMeanRatesValidateLabel.setToolTipText("The model is invalid: At least one substitution rate should be estimated.");
            repaint();
            return;
        }
        if (!isAllClocksAreEqual) {
            fixMeanRatesValidateLabel.setVisible(true);
            fixMeanRatesValidateLabel.m_circleColor = Color.orange;
            fixMeanRatesValidateLabel.setToolTipText("Not all substitution rates 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.getPartitions("SiteModel").size()) {
            fixMeanRatesValidateLabel.setVisible(true);
            fixMeanRatesValidateLabel.m_circleColor = Color.orange;
            fixMeanRatesValidateLabel.setToolTipText("Not all partitions have their rate estimated");
        } else {
            fixMeanRatesValidateLabel.setVisible(false);
        }
        repaint();
    } catch (Exception e) {
        e.printStackTrace();
    }
}