Examples with HierarchicalModelComponentOptions dr.app.beauti.components.hpm.HierarchicalModelComponentOptions used on opensource projects

Example 1 with HierarchicalModelComponentOptions

use of dr.app.beauti.components.hpm.HierarchicalModelComponentOptions in project beast-mcmc by beast-dev.

the class HierarchicalPriorDialog method addHPM.

public void addHPM(java.util.List<Parameter> parameterList) {
    HierarchicalModelComponentOptions comp = (HierarchicalModelComponentOptions) options.getComponentOptions(HierarchicalModelComponentOptions.class);
    HierarchicalPhylogeneticModel hpm = comp.addHPM(nameField.getText(), parameterList, parameterList.get(0).priorType);
    hpm.getConditionalParameterList().get(0).mean = hpmMeanMean;
    hpm.getConditionalParameterList().get(0).stdev = hpmMeanStDev;
    hpm.getConditionalParameterList().get(0).setInitial(hpmMeanInitial);
    hpm.getConditionalParameterList().get(1).shape = hpmPrecShape;
    hpm.getConditionalParameterList().get(1).scale = hpmPrecScale;
    hpm.getConditionalParameterList().get(1).setInitial(hpmPrecInitial);
}

Example 2 with HierarchicalModelComponentOptions

use of dr.app.beauti.components.hpm.HierarchicalModelComponentOptions in project beast-mcmc by beast-dev.

the class PriorsPanel method removeFromJointPrior.

private void removeFromJointPrior(Parameter parameter) {
    LinkedParameterComponentOptions comp = (LinkedParameterComponentOptions) options.getComponentOptions(LinkedParameterComponentOptions.class);
    LinkedParameter linkedParameter = comp.getLinkedParameter(parameter);
    if (linkedParameter != null) {
        comp.removeDependentParameter(parameter);
    }
    // Possibly remove parameter from its HPM
    HierarchicalModelComponentOptions hmco = (HierarchicalModelComponentOptions) options.getComponentOptions(HierarchicalModelComponentOptions.class);
    if (hmco.isHierarchicalParameter(parameter)) {
        if (hmco.removeParameter(this, parameter, true) == JOptionPane.NO_OPTION) {
            // Bail out
            System.err.println("Bailing out of modification");
            return;
        }
        System.err.println("Parameter removed from an HPM");
    }
}

Example 3 with HierarchicalModelComponentOptions

use of dr.app.beauti.components.hpm.HierarchicalModelComponentOptions in project beast-mcmc by beast-dev.

the class PriorsPanel method priorButtonPressed.

private void priorButtonPressed(int row) {
    Parameter parameter = parameters.get(row);
    LinkedParameterComponentOptions lpco = (LinkedParameterComponentOptions) options.getComponentOptions(LinkedParameterComponentOptions.class);
    HierarchicalModelComponentOptions hmco = (HierarchicalModelComponentOptions) options.getComponentOptions(HierarchicalModelComponentOptions.class);
    if (lpco.isArgumentParameter(parameter)) {
        LinkedParameter linkedParameter = lpco.getLinkedParameterForArgument(parameter);
        editLinkedParameter(linkedParameter, linkedParameter.getDependentParameterList());
    } else {
        if (hmco.isHierarchicalParameter(parameter)) {
            int option = JOptionPane.showConfirmDialog(this, "This parameter forms part of an Hierarchical Model.\n" + "Selecting a new prior will remove the parameter from\n" + "this HPM.\nContinue?", "Hierarchical parameter warning", JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE);
            if (option == JOptionPane.NO_OPTION) {
                return;
            }
        }
        if (parameter.isLinked) {
            int option = JOptionPane.showConfirmDialog(this, "Parameter linked to other parameter. Selecting a\n" + "new prior will remove the link.\nContinue?", "Linked parameter warning", JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE);
            if (option == JOptionPane.NO_OPTION) {
                return;
            }
        }
        editPrior(parameter);
    }
}

Example 4 with HierarchicalModelComponentOptions

use of dr.app.beauti.components.hpm.HierarchicalModelComponentOptions in project beast-mcmc by beast-dev.

the class PriorsPanel method hierarchicalButtonPressed.

private void hierarchicalButtonPressed(int[] rows) {
    if (rows.length < 2) {
        JOptionPane.showMessageDialog(frame, "Fewer than two parameters selected.", "Parameter linking error", JOptionPane.WARNING_MESSAGE);
        return;
    }
    Double lowerBound = null;
    Double upperBound = null;
    List<Parameter> paramList = new ArrayList<Parameter>();
    for (int i = 0; i < rows.length; ++i) {
        Parameter parameter = parameters.get(rows[i]);
        if (parameter.isStatistic) {
            JOptionPane.showMessageDialog(frame, "Statistics cannot be used in a hierarchical model.", "HPM parameter linking error", JOptionPane.WARNING_MESSAGE);
            return;
        }
        boolean sameBounds = true;
        if (lowerBound == null) {
            lowerBound = parameter.truncationLower;
        } else {
            if (lowerBound != parameter.truncationLower) {
                sameBounds = false;
            }
        }
        if (upperBound == null) {
            upperBound = parameter.truncationUpper;
        } else {
            if (upperBound != parameter.truncationUpper) {
                sameBounds = false;
            }
        }
        if (!sameBounds) {
            JOptionPane.showMessageDialog(frame, "Only parameters that share the same bounds\n" + "should be included in a HPM.", "HPM parameter link error", JOptionPane.WARNING_MESSAGE);
            // Bail out
            return;
        }
        paramList.add(parameter);
    }
    if (hierarchicalPriorDialog != null) {
        // Already called
        // Check to see if selected parameters are already in a HPM
        HierarchicalModelComponentOptions comp = (HierarchicalModelComponentOptions) options.getComponentOptions(HierarchicalModelComponentOptions.class);
        boolean anyConflicts = false;
        for (Parameter parameter : paramList) {
            if (comp.isHierarchicalParameter(parameter)) {
                anyConflicts = true;
                break;
            }
        }
        if (anyConflicts) {
            int option = JOptionPane.showConfirmDialog(this, "At one selected parameter already exists in a HPM.\n" + "Constructing a new prior will remove these parameter\n" + "from the original model. Continue?", "HPM warning", JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE);
            if (option == JOptionPane.NO_OPTION) {
                return;
            }
        }
    }
    if (hierarchicalPriorDialog == null) {
        hierarchicalPriorDialog = new HierarchicalPriorDialog(frame, options);
    }
    boolean done = false;
    while (!done) {
        int result = hierarchicalPriorDialog.showDialog(paramList);
        if (result == JOptionPane.OK_OPTION && hierarchicalPriorDialog.validateModelName()) {
            hierarchicalPriorDialog.getArguments();
            done = true;
        }
        if (result == JOptionPane.CANCEL_OPTION) {
            return;
        }
    }
    // Remove parameters from old list
    for (Parameter parameter : paramList) {
        HierarchicalModelComponentOptions comp = (HierarchicalModelComponentOptions) options.getComponentOptions(HierarchicalModelComponentOptions.class);
        if (comp.isHierarchicalParameter(parameter)) {
            comp.removeParameter(this, parameter, false);
        }
    }
    // Add HPM to component manager
    hierarchicalPriorDialog.addHPM(paramList);
    for (Parameter parameter : paramList) {
        parameter.setPriorEdited(true);
    }
    priorTableModel.fireTableDataChanged();
}