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Fix hyper-prior support for spec-framework distribution parameters #158

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Fix hyper-prior support for spec-framework distribution parameters #158

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df5048d
suppress vector param domain, shape, keys #155
walterxie Aug 24, 2026
a68f560
Fix estimate checkbox and hyper-prior support for spec-framework dist…
walterxie Aug 24, 2026
560cf13
Use LogUniform to replace OneOnX
walterxie Aug 26, 2026
6b88bc8
fix Dirichlet incorrectly displayed in the Prior panel #160
walterxie Aug 26, 2026
ce33392
correct comments #159
walterxie Aug 26, 2026
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105 changes: 89 additions & 16 deletions beast-fx/src/main/java/beastfx/app/inputeditor/BeautiConfig.java
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@@ -1,25 +1,20 @@
package beastfx.app.inputeditor;



import java.io.File;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Set;

import beastfx.app.util.Alert;
import beastfx.app.util.FXUtils;
import javafx.scene.Parent;
import beast.base.core.BEASTInterface;
import beast.base.core.BEASTObject;
import beast.base.core.Description;
import beast.base.core.Input;
import beast.base.core.Input.Validate;
import beast.base.evolution.alignment.Alignment;
import beast.base.spec.evolution.tree.MRCAPrior;
import beast.base.parser.XMLParser;
import beast.base.spec.evolution.tree.MRCAPrior;
import beastfx.app.util.Alert;
import beastfx.app.util.FXUtils;
import javafx.scene.Parent;

import java.io.File;
import java.util.*;

@Description("Beauti configuration object, used to find Beauti configuration " +
"information from Beauti template files.")
Expand Down Expand Up @@ -92,7 +87,16 @@ public class BeautiConfig extends BEASTObject {
public List<BeautiAlignmentProvider> alignmentProvider;

public BeautiSubTemplate hyperPriorTemplate = null;

/** hyper prior template for spec-framework (RealScalarParam-based) distribution parameters
* whose domain is unbounded Real, e.g. LogNormal's M -- kept separate from hyperPriorTemplate,
* which is still used by the legacy ParameterInputEditor for RealParameter-based priors
* (e.g. when loading an old analysis) */
public BeautiSubTemplate hyperPriorSpecTemplate = null;
/** as hyperPriorSpecTemplate, but for PositiveReal/NonNegativeReal-domain parameters, e.g.
* LogNormal's S -- a Normal prior would be domain-incompatible with such a parameter (it
* would show as an invalid/mismatched entry in the distribution dropdown) */
public BeautiSubTemplate hyperPriorSpecPositiveTemplate = null;

@Override
public void initAndValidate() {
parseSet(inlineInput.get(), null, inlineBEASTObject);
Expand Down Expand Up @@ -123,8 +127,12 @@ public void initAndValidate() {
alignmentProvider = alignmentProviderInput.get();

try {
XMLParser parser = new XMLParser();
hyperPriorTemplate = (BeautiSubTemplate) parser.parseBareFragment(HYPER_PRIOR_XML, true);
// a fresh XMLParser per fragment -- the parser keeps mutable DOM state
// internally, and reusing one instance across multiple parseBareFragment()
// calls corrupts the second parse (stray "]]>" CDATA-boundary errors)
hyperPriorTemplate = (BeautiSubTemplate) new XMLParser().parseBareFragment(HYPER_PRIOR_XML, true);
hyperPriorSpecTemplate = (BeautiSubTemplate) new XMLParser().parseBareFragment(HYPER_PRIOR_SPEC_XML, true);
hyperPriorSpecPositiveTemplate = (BeautiSubTemplate) new XMLParser().parseBareFragment(HYPER_PRIOR_SPEC_POSITIVE_XML, true);
} catch (Exception e) {
// TODO Auto-generated catch block
e.printStackTrace();
Expand Down Expand Up @@ -153,14 +161,79 @@ public void initAndValidate() {
" <connect spec='beastfx.app.inputeditor.BeautiConnector' srcID='HyperPrior.$(n)' targetID='prior' inputName='distribution' if='inposterior(parameter.$(n)) and parameter.$(n)/estimate=true'>Hyper prior for parameter $(n)</connect>\n" +
" </subtemplate>\n" +
" </beast>\n";


/**
* Hyper prior for a spec-framework distribution's own parameter whose domain is unbounded
* Real (e.g. LogNormal's M). Unlike the legacy template above, the distribution is connected
* to 'prior' directly (there is no wrapping Prior object any more). A Normal + random walk is
* used since the target's domain is not restricted to positive values, unlike the legacy
* OneOnX (which has no spec equivalent) + multiplicative ScaleOperator.
*/
final static String HYPER_PRIOR_SPEC_XML =
" <beast version='2.8'\n" +
" namespace='beastfx.app.beauti:beast.base.core'>\n" +
" <!-- Parameter Hyper Prior for spec-framework distribution parameters -->\n" +
" <subtemplate spec='beastfx.app.inputeditor.BeautiSubTemplate' id='HyperPriorSpec' class='beast.base.spec.inference.distribution.Normal' mainid='HyperPriorSpec.$(n)'>\n" +
" <![CDATA[\n" +
" <distribution id='HyperPriorSpec.$(n)' spec='beast.base.spec.inference.distribution.Normal' param='@parameter.$(n)'>\n" +
" <sigma spec='beast.base.spec.inference.parameter.RealScalarParam' domain='PositiveReal' value='10.0' estimate='false'/>\n" +
" </distribution>\n" +
"\n" +
" <operator id='hyperRandomWalk.$(n)' spec='beast.base.spec.inference.operator.RealRandomWalkOperator' scalar='@parameter.$(n)' windowSize='1' weight='0.1'/>\n" +
" ]]>\n" +
" <connect spec='beastfx.app.inputeditor.BeautiConnector' srcID='parameter.$(n)' targetID='state' inputName='stateNode' if='inposterior(parameter.$(n)) and parameter.$(n)/estimate=true'/>\n" +
"\n" +
" <connect spec='beastfx.app.inputeditor.BeautiConnector' srcID='hyperRandomWalk.$(n)' targetID='mcmc' inputName='operator' if='inposterior(parameter.$(n)) and parameter.$(n)/estimate=true'>Random walk on hyper parameter $(n)</connect>\n" +
"\n" +
" <connect spec='beastfx.app.inputeditor.BeautiConnector' srcID='parameter.$(n)' targetID='tracelog' inputName='log' if='inposterior(parameter.$(n)) and parameter.$(n)/estimate=true'/>\n" +
" <connect spec='beastfx.app.inputeditor.BeautiConnector' srcID='HyperPriorSpec.$(n)' targetID='tracelog' inputName='log' if='inposterior(parameter.$(n)) and parameter.$(n)/estimate=true'/>\n" +
"\n" +
" <connect spec='beastfx.app.inputeditor.BeautiConnector' srcID='HyperPriorSpec.$(n)' targetID='prior' inputName='distribution' if='inposterior(parameter.$(n)) and parameter.$(n)/estimate=true'>Hyper prior for parameter $(n)</connect>\n" +
" </subtemplate>\n" +
" </beast>\n";

/**
* As HYPER_PRIOR_SPEC_XML, but for a PositiveReal/NonNegativeReal-domain parameter (e.g.
* LogNormal's S, Gamma's alpha/theta). A Normal prior is domain-incompatible with such a
* parameter (it would show as a mismatched entry outside the compatible-domain dropdown list
* in the Priors panel -- see ScalarDistributionInputEditor.isCompatible), so a Gamma is used
* instead, matching the weak/vague-prior convention already used elsewhere in Standard.xml
* (e.g. MutationRatePrior, ClockPrior, YuleBirthRatePrior), together with the same
* multiplicative ScaleOperator used for other PositiveReal-domain parameters.
*/
final static String HYPER_PRIOR_SPEC_POSITIVE_XML =
" <beast version='2.8'\n" +
" namespace='beastfx.app.beauti:beast.base.core'>\n" +
" <!-- Parameter Hyper Prior for spec-framework PositiveReal/NonNegativeReal-domain distribution parameters -->\n" +
" <subtemplate spec='beastfx.app.inputeditor.BeautiSubTemplate' id='HyperPriorSpecPositive' class='beast.base.spec.inference.distribution.Gamma' mainid='HyperPriorSpecPositive.$(n)'>\n" +
" <![CDATA[\n" +
" <distribution id='HyperPriorSpecPositive.$(n)' spec='beast.base.spec.inference.distribution.Gamma' param='@parameter.$(n)'>\n" +
" <alpha spec='beast.base.spec.inference.parameter.RealScalarParam' domain='PositiveReal' value='0.001' estimate='false'/>\n" +
" <theta spec='beast.base.spec.inference.parameter.RealScalarParam' domain='PositiveReal' value='1000.0' estimate='false'/>\n" +
" </distribution>\n" +
"\n" +
" <operator id='hyperScaler.$(n)' spec='beast.base.spec.inference.operator.ScaleOperator' scaleFactor='0.5' weight='0.1' parameter='@parameter.$(n)'/>\n" +
" ]]>\n" +
" <connect spec='beastfx.app.inputeditor.BeautiConnector' srcID='parameter.$(n)' targetID='state' inputName='stateNode' if='inposterior(parameter.$(n)) and parameter.$(n)/estimate=true'/>\n" +
"\n" +
" <connect spec='beastfx.app.inputeditor.BeautiConnector' srcID='hyperScaler.$(n)' targetID='mcmc' inputName='operator' if='inposterior(parameter.$(n)) and parameter.$(n)/estimate=true'>Scale hyper parameter $(n)</connect>\n" +
"\n" +
" <connect spec='beastfx.app.inputeditor.BeautiConnector' srcID='parameter.$(n)' targetID='tracelog' inputName='log' if='inposterior(parameter.$(n)) and parameter.$(n)/estimate=true'/>\n" +
" <connect spec='beastfx.app.inputeditor.BeautiConnector' srcID='HyperPriorSpecPositive.$(n)' targetID='tracelog' inputName='log' if='inposterior(parameter.$(n)) and parameter.$(n)/estimate=true'/>\n" +
"\n" +
" <connect spec='beastfx.app.inputeditor.BeautiConnector' srcID='HyperPriorSpecPositive.$(n)' targetID='prior' inputName='distribution' if='inposterior(parameter.$(n)) and parameter.$(n)/estimate=true'>Hyper prior for parameter $(n)</connect>\n" +
" </subtemplate>\n" +
" </beast>\n";

public void setDoc(BeautiDoc doc) {
partitionTemplate.get().setDoc(doc);
for (BeautiSubTemplate sub : subTemplates) {
sub.setDoc(doc);
}
doc.setExpertMode(isExpertInput.get());
hyperPriorTemplate.doc = doc;
hyperPriorSpecTemplate.doc = doc;
hyperPriorSpecPositiveTemplate.doc = doc;
}

public void clear() {
Expand Down
2 changes: 2 additions & 0 deletions beast-fx/src/main/java/beastfx/app/inputeditor/BeautiDoc.java
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Expand Up @@ -1632,6 +1632,8 @@ synchronized public void scrubAll(boolean useNotEstimatedStateNodes, boolean isI

List<BeautiSubTemplate> templates = new ArrayList<>();
templates.add(beautiConfig.hyperPriorTemplate);
templates.add(beautiConfig.hyperPriorSpecTemplate);
templates.add(beautiConfig.hyperPriorSpecPositiveTemplate);
for (BEASTInterface beastObject : pluginmap.values()) {
if (beastObject instanceof StateNode) {
if (beastObject.getID() != null && beastObject.getID().startsWith("parameter.")) {
Expand Down
67 changes: 39 additions & 28 deletions beast-fx/src/main/java/beastfx/app/inputeditor/spec/ScalarInputEditor.java
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Original file line number Diff line number Diff line change
@@ -1,24 +1,21 @@
package beastfx.app.inputeditor.spec;



import beast.base.core.BEASTInterface;
import beast.base.core.Input;
import beast.base.core.Log;
import beast.base.evolution.branchratemodel.BranchRateModel;
import beast.base.inference.Distribution;
import beast.base.inference.Operator;
import beast.base.inference.StateNode;
import beast.base.parser.PartitionContext;
import beast.base.spec.domain.NonNegativeReal;
import beast.base.spec.domain.PositiveReal;
import beast.base.spec.inference.distribution.ScalarDistribution;
import beast.base.spec.inference.parameter.BoolScalarParam;
import beast.base.spec.inference.parameter.IntScalarParam;
import beast.base.spec.inference.parameter.RealScalarParam;
import beast.base.spec.type.Scalar;
import beastfx.app.inputeditor.BEASTObjectDialog;
import beastfx.app.inputeditor.BEASTObjectInputEditor;
import beastfx.app.inputeditor.BEASTObjectPanel;
import beastfx.app.inputeditor.BeautiDoc;
import beastfx.app.inputeditor.*;
import beastfx.app.util.Alert;
import beastfx.app.util.FXUtils;
import javafx.geometry.Insets;
Expand All @@ -32,9 +29,6 @@
import java.util.List;





public class ScalarInputEditor extends BEASTObjectInputEditor {
boolean isParametricDistributionParameter = false;

Expand Down Expand Up @@ -212,7 +206,9 @@ protected void addComboBox(Pane box, Input<?> input, BEASTInterface beastObject)
//m_bAddButtons = false;
if (itemNr < 0) {
for (Object beastObject2 : ((BEASTInterface) m_input.get()).getOutputs()) {
if (beastObject2 instanceof RealScalarParam) {
// a distribution whose *own* parameter (mean, sigma, alpha, ...) this is,
// as opposed to a distribution for which this is the target (paramInput)
if (beastObject2 instanceof ScalarDistribution<?,?> sd && sd.paramInput.get() != parameter) {
m_isEstimatedBox.setVisible(doc.allowLinking);
m_isEstimatedBox.setVisible(true);
isParametricDistributionParameter = true;
Expand Down Expand Up @@ -259,39 +255,54 @@ public void toggleEstimate() {
}

String id = parameter2.getID();


if (id.startsWith("RealParameter")) {
ScalarDistribution<?,?> parent = null;
// generalises the legacy "RealParameter" prefix check: any parameter that
// hasn't already been given a "parameter.<context>" id (spec params default
// to e.g. "RealScalarParam.N", not "RealParameter.N") needs one, so that
// $(n) substitution below and BeautiDoc's general "parameter.*" sync scan
// (see BeautiDoc.applyBeautiRules) can find it
if (id == null || !id.startsWith("parameter.")) {
ScalarDistribution<?,?> parent = null;
for (Object beastObject2 : parameter2.getOutputs()) {
if (beastObject2 instanceof ScalarDistribution<?,?>) {
parent = (ScalarDistribution<?,?>) beastObject2;
break;
}
}
Distribution grandparent = null;
for (Object beastObject2 : parent.getOutputs()) {
if (beastObject2 instanceof Distribution) {
grandparent = (Distribution) beastObject2;
if (beastObject2 instanceof ScalarDistribution<?,?> sd && sd.paramInput.get() != parameter2) {
parent = sd;
break;
}
}
id = "parameter.hyper" + parent.getClass().getSimpleName() + "-" +
m_input.getName() + "-" + grandparent.getID();
if (parent == null) {
Log.err.println("Could not find the distribution owning " + parameter2.getID() + "; not adding a hyperprior");
m_isEstimatedBox.setSelected(false);
parameter2.isEstimatedInput.setValue(false, parameter2);
return;
}
// parent's own id is already partition-specific in the spec framework
// (e.g. "ClockPrior.c:1stpos", connected directly into 'prior') -- there
// is no separate wrapping Prior object to look up any more
id = "parameter.hyper" + parent.getClass().getSimpleName() + "-" +
m_input.getName() + "-" + parent.getID();
doc.pluginmap.remove(parameter2.getID());
parameter2.setID(id);
doc.addPlugin(parameter2);
}



PartitionContext context = new PartitionContext(id.substring("parameter.".length()));
Log.warning.println(context + " " + id);
doc.beautiConfig.hyperPriorTemplate.createSubNet(context, true);

// the default hyperprior distribution must be domain-compatible with the
// parameter it is applied to, or it shows up as a mismatched entry outside
// the compatible-domain dropdown list in the Priors panel (see
// ScalarDistributionInputEditor.isCompatible)
boolean isPositive = parameter2 instanceof RealScalarParam<?> realParam &&
(realParam.getDomain() instanceof PositiveReal || realParam.getDomain() instanceof NonNegativeReal);
BeautiSubTemplate hyperTemplate = isPositive ?
doc.beautiConfig.hyperPriorSpecPositiveTemplate :
doc.beautiConfig.hyperPriorSpecTemplate;
hyperTemplate.createSubNet(context, true);
}
hardSync();
refreshPanel();
} catch (Exception ex) {
Log.err.println("ParameterInputEditor " + ex.getMessage());
Log.err.println("ScalarInputEditor " + ex.getMessage());
}
}

Expand Down
24 changes: 17 additions & 7 deletions beast-fx/src/main/resources/beast.fx/fxtemplates/ParametricDistributions.xml
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Expand Up @@ -33,13 +33,6 @@
]]>
</subtemplate>

<!-- OneOnX -->
<subtemplate id='1/X' class='beast.base.inference.distribution.OneOnX' mainid='[top]'>
<![CDATA[
<distr spec="beast.base.inference.distribution.OneOnX"/>
]]>
</subtemplate>

<!-- lognormal -->
<subtemplate id='LogNormal' class='beast.base.spec.inference.distribution.LogNormal' mainid='[top]'
suppressInputs='beast.base.spec.inference.distribution.LogNormal.param'
Expand Down Expand Up @@ -188,6 +181,21 @@
]]>
</subtemplate>

<!-- OneOnX (improper 1/x prior) is removed from the BEAUti distribution list; -->
<!-- use LogUniform as a replacement to a PositiveReal-domain param bounded on [lower, upper]. -->
<subtemplate id='LogUniform' class='beast.base.spec.inference.distribution.LogUniform' mainid='[top]'
suppressInputs='beast.base.spec.inference.distribution.LogUniform.param'
hmc='
LogUniform/lower/=ParametricDistributions/LogUniform/lower/,
LogUniform/upper/=ParametricDistributions/LogUniform/upper/'>
<![CDATA[
<distr spec="beast.base.spec.inference.distribution.LogUniform">
<lower spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal" value="1.0E-8" estimate="false"/>
<upper spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal" value="1.0E8" estimate="false"/>
</distr>
]]>
</subtemplate>

<!-- Poisson -->
<subtemplate id='Poisson' class='beast.base.spec.inference.distribution.Poisson' mainid='[top]'
suppressInputs='beast.base.spec.inference.distribution.Poisson.param'
Expand All @@ -202,11 +210,13 @@

<!-- Dirichlet -->
<subtemplate id='Dirichlet' class='beast.base.spec.inference.distribution.Dirichlet' mainid='[top]'
suppressInputs='beast.base.spec.inference.distribution.Dirichlet.param'
hmc='
Dirichlet/alpha/=ParametricDistributions/Dirichlet/mean/,
Dirichlet/offset/=ParametricDistributions/Dirichlet/offset/'>
<![CDATA[
<distr spec="beast.base.spec.inference.distribution.Dirichlet">
<param spec="beast.base.spec.inference.parameter.SimplexParam" dimension="1" value="1.0" estimate="false"/>
<alpha spec="beast.base.spec.inference.parameter.RealVectorParam" domain="PositiveReal" estimate="false">1.0</alpha>
</distr>
]]>
Expand Down
12 changes: 12 additions & 0 deletions beast-fx/src/main/resources/beast.fx/fxtemplates/Standard.xml
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Expand Up @@ -126,6 +126,18 @@
beast.base.spec.inference.parameter.IntScalarParam.domain,
beast.base.spec.inference.parameter.RealVectorParam.domain,
beast.base.spec.inference.parameter.IntVectorParam.domain,
beast.base.spec.inference.parameter.RealVectorParam.shape,
beast.base.spec.inference.parameter.RealVectorParam.keys,
beast.base.spec.inference.parameter.IntVectorParam.shape,
beast.base.spec.inference.parameter.IntVectorParam.keys,
beast.base.spec.inference.parameter.BoolVectorParam.shape,
beast.base.spec.inference.parameter.BoolVectorParam.keys,
beast.base.spec.inference.parameter.SimplexParam.domain,
beast.base.spec.inference.parameter.SimplexParam.shape,
beast.base.spec.inference.parameter.SimplexParam.keys,
beast.base.spec.inference.parameter.IntSimplexParam.domain,
beast.base.spec.inference.parameter.IntSimplexParam.shape,
beast.base.spec.inference.parameter.IntSimplexParam.keys,
beast.base.spec.inference.distribution.IID.param,
beast.base.spec.inference.distribution.MarkovChainDistribution.param
'
Expand Down
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