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Fix several simple bugs in Prior panel #161

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Merged
rbouckaert merged 6 commits into from
Aug 30, 2026
Merged

Fix several simple bugs in Prior panel #161

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beba5a4
Use LogUniform to replace OneOnX
walterxie Aug 26, 2026
d7766f6
fix Dirichlet incorrectly displayed in the Prior panel #160
walterxie Aug 26, 2026
c6093be
correct comments #159
walterxie Aug 26, 2026
ebb69b9
fix param type incorrectly passed to BEASTObjectDialog during init in…
walterxie Aug 26, 2026
252d162
a proper fix to distinguish vector paramDomain == Real.class with Dir…
walterxie Aug 27, 2026
4814452
comment on Dirichlet template #160
walterxie Aug 28, 2026
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55 changes: 28 additions & 27 deletions beast-fx/src/main/java/beastfx/app/inputeditor/IIDInputEditor.java
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Original file line number Diff line number Diff line change
@@ -1,38 +1,19 @@
package beastfx.app.inputeditor;







import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;

import beast.base.core.BEASTInterface;
import beast.base.core.Input;
import beast.base.inference.Distribution;
import beast.base.parser.PartitionContext;
import beast.base.spec.domain.Int;
import beast.base.spec.domain.NonNegativeInt;
import beast.base.spec.domain.NonNegativeReal;
import beast.base.spec.domain.PositiveInt;
import beast.base.spec.domain.PositiveReal;
import beast.base.spec.domain.Real;
import beast.base.spec.domain.*;
import beast.base.spec.inference.distribution.IID;
import beast.base.spec.inference.distribution.ScalarDistribution;
import beast.base.spec.inference.distribution.TensorDistribution;
import beast.base.spec.inference.parameter.BoolScalarParam;
import beast.base.spec.inference.parameter.IntScalarParam;
import beast.base.spec.inference.parameter.IntVectorParam;
import beast.base.spec.inference.parameter.RealScalarParam;
import beast.base.spec.inference.parameter.RealVectorParam;
import beast.base.spec.type.IntScalar;
import beast.base.spec.inference.parameter.*;
import beast.base.spec.type.IntVector;
import beast.base.spec.type.RealScalar;
import beast.base.spec.type.RealVector;
import beast.base.spec.type.Scalar;
import beast.base.spec.type.Simplex;
import beastfx.app.util.FXUtils;
import javafx.geometry.Insets;
import javafx.scene.Node;
Expand All @@ -43,6 +24,10 @@
import javafx.scene.layout.HBox;
import javafx.scene.layout.Pane;

import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;

public class IIDInputEditor extends ScalarDistributionInputEditor {

public IIDInputEditor() {
Expand Down Expand Up @@ -118,7 +103,7 @@ public void init(Input<?> input, BEASTInterface beastObject, int itemNr, ExpandO
List<?> list = (List<?>) m_input.get();
TensorDistribution<?,?> prior1 = (TensorDistribution<?,?>) list.get(itemNr);
BEASTInterface p1 = (BEASTInterface) prior1.paramInput.get();
BEASTObjectDialog dlg = new BEASTObjectDialog(p1, RealScalar.class, doc);
BEASTObjectDialog dlg = new BEASTObjectDialog(p1, p1.getClass(), doc);
if (dlg.showDialog()) {
dlg.accept(p1, doc);
((BEASTInterface)p1).initAndValidate();
Expand All @@ -139,7 +124,7 @@ public void init(Input<?> input, BEASTInterface beastObject, int itemNr, ExpandO
List<?> list = (List<?>) m_input.get();
TensorDistribution<?,?> prior1 = (TensorDistribution<?,?>) list.get(itemNr);
BEASTInterface p1 = (BEASTInterface) prior1.paramInput.get();
BEASTObjectDialog dlg = new BEASTObjectDialog(p1, IntScalar.class, doc);
BEASTObjectDialog dlg = new BEASTObjectDialog(p1, p1.getClass(), doc);
if (dlg.showDialog()) {
dlg.accept(p1, doc);
p1.initAndValidate();
Expand Down Expand Up @@ -273,9 +258,10 @@ protected ComboBox<BeautiSubTemplate> createComboBox() {
Object param = distr.paramInput.get();
Class<?> domain = getParameterDomain(param);
for (BeautiSubTemplate template : tensorTemplates) {
if (isCompatible(domain, templateDomains.get(k++))) {
if (isCompatible(domain, templateDomains.get(k), hasSimplexParam(param, templateInstances.get(k)))) {
comboBox.getItems().add(template);
}
k++;
}

if (comboBox.getItems().size() == 0) {
Expand Down Expand Up @@ -353,12 +339,27 @@ protected void updateItem(BeautiSubTemplate item, boolean empty) {
}


private boolean isCompatible(Class<?> paramDomain, Class<?> templateDomain) {
/**
* Domain range checks in isCompatible() can't see the "elements sum to 1" structural
* constraint of a Simplex, so a Simplex-only template must line up with a
* Simplex-valued param, and a non-Simplex template must not be offered for one.
*/
private boolean hasSimplexParam(Object param, TensorDistribution<?,?> templateInstance) {
Object templateParam = templateInstance == null ? null : templateInstance.getInput("param").get();
boolean paramIsSimplex = param instanceof Simplex;
boolean templateIsSimplex = templateParam instanceof Simplex;
return paramIsSimplex == templateIsSimplex;
}

private boolean isCompatible(Class<?> paramDomain, Class<?> templateDomain, boolean hasSimplexParam) {
if (templateDomain == null) {
// the "no prior" and ScalarDistribution templates should be rejected
return false;
}

if (!hasSimplexParam) {
return false;
}

if (Real.class.isAssignableFrom(paramDomain)) {
// check type first
if (!(Real.class.isAssignableFrom(templateDomain))) {
Expand Down
4 changes: 2 additions & 2 deletions beast-fx/src/main/java/beastfx/app/inputeditor/ScalarDistributionInputEditor.java
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Original file line number Diff line number Diff line change
Expand Up @@ -165,7 +165,7 @@ public void init(Input<?> input, BEASTInterface beastObject, int itemNr, ExpandO
return;
}
BEASTInterface p1 = (BEASTInterface) prior1.paramInput.get();
BEASTObjectDialog dlg = new BEASTObjectDialog(p1, RealScalar.class, doc);
BEASTObjectDialog dlg = new BEASTObjectDialog(p1, p1.getClass(), doc);
if (dlg.showDialog()) {
dlg.accept(p1, doc);
((BEASTInterface)p1).initAndValidate();
Expand All @@ -188,7 +188,7 @@ public void init(Input<?> input, BEASTInterface beastObject, int itemNr, ExpandO
return;
}
BEASTInterface p1 = (BEASTInterface) prior1.paramInput.get();
BEASTObjectDialog dlg = new BEASTObjectDialog(p1, IntScalar.class, doc);
BEASTObjectDialog dlg = new BEASTObjectDialog(p1, p1.getClass(), doc);
if (dlg.showDialog()) {
dlg.accept(p1, doc);
p1.initAndValidate();
Expand Down
31 changes: 25 additions & 6 deletions beast-fx/src/main/java/beastfx/app/inputeditor/TensorDistributionInputEditor.java
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,10 @@
import beast.base.spec.inference.distribution.ScalarDistribution;
import beast.base.spec.inference.distribution.TensorDistribution;
import beast.base.spec.inference.parameter.*;
import beast.base.spec.type.*;
import beast.base.spec.type.IntVector;
import beast.base.spec.type.RealVector;
import beast.base.spec.type.Scalar;
import beast.base.spec.type.Simplex;
import beastfx.app.util.FXUtils;
import javafx.scene.Node;
import javafx.scene.control.Button;
Expand Down Expand Up @@ -98,7 +101,7 @@ public void init(Input<?> input, BEASTInterface beastObject, int itemNr, ExpandO
List<?> list = (List<?>) m_input.get();
TensorDistribution<?,?> prior1 = (TensorDistribution<?,?>) list.get(itemNr);
BEASTInterface p1 = (BEASTInterface) prior1.paramInput.get();
BEASTObjectDialog dlg = new BEASTObjectDialog(p1, RealScalar.class, doc);
BEASTObjectDialog dlg = new BEASTObjectDialog(p1, p1.getClass(), doc);
if (dlg.showDialog()) {
dlg.accept(p1, doc);
((BEASTInterface)p1).initAndValidate();
Expand All @@ -119,7 +122,7 @@ public void init(Input<?> input, BEASTInterface beastObject, int itemNr, ExpandO
List<?> list = (List<?>) m_input.get();
TensorDistribution<?,?> prior1 = (TensorDistribution<?,?>) list.get(itemNr);
BEASTInterface p1 = (BEASTInterface) prior1.paramInput.get();
BEASTObjectDialog dlg = new BEASTObjectDialog(p1, IntScalar.class, doc);
BEASTObjectDialog dlg = new BEASTObjectDialog(p1, p1.getClass(), doc);
if (dlg.showDialog()) {
dlg.accept(p1, doc);
p1.initAndValidate();
Expand Down Expand Up @@ -253,9 +256,10 @@ private ComboBox<BeautiSubTemplate> createComboBox() {
Object param = distr.paramInput.get();
Class<?> domain = getParameterDomain(param);
for (BeautiSubTemplate template : tensorTemplates) {
if (isCompatible(domain, templateDomains.get(k++))) {
if (isCompatible(domain, templateDomains.get(k), hasSimplexParam(param, templateInstances.get(k)))) {
comboBox.getItems().add(template);
}
k++;
}

if (comboBox.getItems().size() == 0) {
Expand Down Expand Up @@ -334,12 +338,27 @@ protected void updateItem(BeautiSubTemplate item, boolean empty) {
}


private boolean isCompatible(Class<?> paramDomain, Class<?> templateDomain) {
/**
* Domain range checks in isCompatible() can't see the "elements sum to 1" structural
* constraint of a Simplex, so a Simplex-only template must line up with a
* Simplex-valued param, and a non-Simplex template must not be offered for one.
*/
private boolean hasSimplexParam(Object param, TensorDistribution<?,?> templateInstance) {
Object templateParam = templateInstance == null ? null : templateInstance.getInput("param").get();
boolean paramIsSimplex = param instanceof Simplex;
boolean templateIsSimplex = templateParam instanceof Simplex;
return paramIsSimplex == templateIsSimplex;
}

private boolean isCompatible(Class<?> paramDomain, Class<?> templateDomain, boolean hasSimplexParam) {
if (templateDomain == null) {
// the "no prior" and ScalarDistribution templates should be rejected
return false;
}

if (!hasSimplexParam) {
return false;
}

if (Real.class.isAssignableFrom(paramDomain)) {
// check type first
if (!(Real.class.isAssignableFrom(templateDomain))) {
Expand Down
27 changes: 20 additions & 7 deletions beast-fx/src/main/resources/beast.fx/fxtemplates/ParametricDistributions.xml
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Original file line number Diff line number Diff line change
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 @@ -201,12 +209,17 @@
</subtemplate>

<!-- Dirichlet -->
<!-- The "param" below is hidden from the user (see suppressInputs) and its value is never used. -->
<!-- BEAUti still needs it to recognize Dirichlet as a valid prior for simplex parameters; -->
<!-- without it, Dirichlet would disappear from the prior dropdown. -->
<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
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