Examples with RealParameter beast.core.parameter.RealParameter used on opensource projects

Example 76 with RealParameter

use of beast.core.parameter.RealParameter in project beast2 by CompEvol.

the class EmpiricalSubstitutionModel method getEmpericalFrequencieValues.

/**
 * convert empirical frequencies into a RealParameter *
 */
Frequencies getEmpericalFrequencieValues() {
    double[] freqs = getEmpiricalFrequencies();
    int[] order = getEncodingOrder();
    int states = freqs.length;
    Frequencies freqsParam = new Frequencies();
    String valuesString = "";
    for (int i = 0; i < states; i++) {
        valuesString += freqs[order[i]] + " ";
    }
    RealParameter freqsRParam = new RealParameter();
    freqsRParam.initByName("value", valuesString, "lower", 0.0, "upper", 1.0, "dimension", states);
    freqsParam.frequenciesInput.setValue(freqsRParam, freqsParam);
    freqsParam.initAndValidate();
    return freqsParam;
}

Example 77 with RealParameter

use of beast.core.parameter.RealParameter in project beast2 by CompEvol.

the class ClusterTree method initAndValidate.

@Override
public void initAndValidate() {
    RealParameter clockRate = clockRateInput.get();
    if (dataInput.get() != null) {
        taxaNames = dataInput.get().getTaxaNames();
    } else {
        if (m_taxonset.get() == null) {
            throw new RuntimeException("At least one of taxa and taxonset input needs to be specified");
        }
        taxaNames = m_taxonset.get().asStringList();
    }
    if (Boolean.valueOf(System.getProperty("beast.resume")) && (isEstimatedInput.get() || (m_initial.get() != null && m_initial.get().isEstimatedInput.get()))) {
        // don't bother creating a cluster tree to save some time, if it is read from file anyway
        // make a caterpillar
        Node left = newNode();
        left.setNr(0);
        left.setID(taxaNames.get(0));
        left.setHeight(0);
        for (int i = 1; i < taxaNames.size(); i++) {
            final Node right = newNode();
            right.setNr(i);
            right.setID(taxaNames.get(i));
            right.setHeight(0);
            final Node parent = newNode();
            parent.setNr(taxaNames.size() + i - 1);
            parent.setHeight(i);
            left.setParent(parent);
            parent.setLeft(left);
            right.setParent(parent);
            parent.setRight(right);
            left = parent;
        }
        root = left;
        leafNodeCount = taxaNames.size();
        nodeCount = leafNodeCount * 2 - 1;
        internalNodeCount = leafNodeCount - 1;
        super.initAndValidate();
        return;
    }
    distance = distanceInput.get();
    if (distance == null) {
        distance = new JukesCantorDistance();
    }
    if (distance instanceof Distance.Base) {
        if (dataInput.get() == null) {
        // Distance requires an alignment?
        }
        ((Distance.Base) distance).setPatterns(dataInput.get());
    }
    linkType = clusterTypeInput.get();
    if (linkType == Type.upgma)
        linkType = Type.average;
    if (linkType == Type.neighborjoining || linkType == Type.neighborjoining2) {
        distanceIsBranchLength = true;
    }
    final Node root = buildClusterer();
    setRoot(root);
    root.labelInternalNodes((getNodeCount() + 1) / 2);
    super.initAndValidate();
    if (linkType == Type.neighborjoining2) {
        // set tip dates to zero
        final Node[] nodes = getNodesAsArray();
        for (int i = 0; i < getLeafNodeCount(); i++) {
            nodes[i].setHeight(0);
        }
        super.initAndValidate();
    }
    if (m_initial.get() != null)
        processTraits(m_initial.get().m_traitList.get());
    else
        processTraits(m_traitList.get());
    if (timeTraitSet != null)
        adjustTreeNodeHeights(root);
    else {
        // all nodes should be at zero height if no date-trait is available
        for (int i = 0; i < getLeafNodeCount(); i++) {
            getNode(i).setHeight(0);
        }
    }
    // divide all node heights by clock rate to convert from substitutions to time.
    for (Node node : getInternalNodes()) {
        double height = node.getHeight();
        node.setHeight(height / clockRate.getValue());
    }
    initStateNodes();
}

Example 78 with RealParameter

use of beast.core.parameter.RealParameter in project beast2 by CompEvol.

the class FrequenciesInputEditor method addComboBox.

// init
@Override
protected /**
 * suppress combobox *
 */
void addComboBox(JComponent box, Input<?> input, BEASTInterface beastObject) {
    Frequencies freqs = (Frequencies) input.get();
    JComboBox<String> comboBox = new JComboBox<>(new String[] { "Estimated", "Empirical", "All equal" });
    if (freqs.frequenciesInput.get() != null) {
        comboBox.setSelectedIndex(0);
        freqsParameter = freqs.frequenciesInput.get();
        alignment = (Alignment) getCandidate(freqs.dataInput, freqs);
    } else if (freqs.estimateInput.get()) {
        comboBox.setSelectedIndex(1);
        alignment = freqs.dataInput.get();
        freqsParameter = (RealParameter) getCandidate(freqs.frequenciesInput, freqs);
    } else {
        comboBox.setSelectedIndex(2);
        alignment = freqs.dataInput.get();
        freqsParameter = (RealParameter) getCandidate(freqs.frequenciesInput, freqs);
    }
    comboBox.addActionListener(e -> {
        // @SuppressWarnings("unchecked")
        // JComboBox<String> comboBox = (JComboBox<String>) e.getSource();
        int selected = comboBox.getSelectedIndex();
        // Frequencies freqs = (Frequencies) m_input.get();
        try {
            switch(selected) {
                case 0:
                    freqs.frequenciesInput.setValue(freqsParameter, freqs);
                    freqs.dataInput.setValue(null, freqs);
                    break;
                case 1:
                    freqs.frequenciesInput.setValue(null, freqs);
                    freqs.dataInput.setValue(alignment, freqs);
                    freqs.estimateInput.setValue(true, freqs);
                    break;
                case 2:
                    freqs.frequenciesInput.setValue(null, freqs);
                    freqs.dataInput.setValue(alignment, freqs);
                    freqs.estimateInput.setValue(false, freqs);
                    break;
            }
        } catch (Exception e2) {
            e2.printStackTrace();
        }
    // System.err.println(freqs.frequencies.get() + " " + freqs.m_data.get() + " " + freqs.m_bEstimate.get());
    });
    box.add(comboBox);
}

Example 79 with RealParameter

use of beast.core.parameter.RealParameter in project beast2 by CompEvol.

the class SiteModelInputEditor method processEntry2.

void processEntry2() {
    String categories = categoryCountEntry.getText();
    try {
        int categoryCount = Integer.parseInt(categories);
        RealParameter shapeParameter = ((SiteModel) m_input.get()).shapeParameterInput.get();
        if (!gammaShapeEditor.getComponent().isVisible() && categoryCount >= 2) {
            // we are flipping from no gamma to gamma heterogeneity accross sites
            // so set the estimate flag on the shape parameter
            shapeParameter.isEstimatedInput.setValue(true, shapeParameter);
        } else if (gammaShapeEditor.getComponent().isVisible() && categoryCount < 2) {
            // we are flipping from with gamma to no gamma heterogeneity accross sites
            // so unset the estimate flag on the shape parameter
            shapeParameter.isEstimatedInput.setValue(false, shapeParameter);
        }
        Object o = ((ParameterInputEditor) gammaShapeEditor).getComponent();
        if (o instanceof ParameterInputEditor) {
            ParameterInputEditor e = (ParameterInputEditor) o;
            e.m_isEstimatedBox.setSelected(shapeParameter.isEstimatedInput.get());
        }
        gammaShapeEditor.getComponent().setVisible(categoryCount >= 2);
        repaint();
    } catch (java.lang.NumberFormatException e) {
    // ignore.
    }
}

Example 80 with RealParameter

use of beast.core.parameter.RealParameter 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();
    }
}