diff --git a/beast-fx/src/main/java/beastfx/app/inputeditor/TensorDistributionInputEditor.java b/beast-fx/src/main/java/beastfx/app/inputeditor/TensorDistributionInputEditor.java
index c934f633..e48fcd12 100644
--- a/beast-fx/src/main/java/beastfx/app/inputeditor/TensorDistributionInputEditor.java
+++ b/beast-fx/src/main/java/beastfx/app/inputeditor/TensorDistributionInputEditor.java
@@ -1,37 +1,15 @@
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.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.type.IntVector;
-import beast.base.spec.type.RealScalar;
-import beast.base.spec.type.RealVector;
-import beast.base.spec.type.Scalar;
+import beast.base.spec.inference.parameter.*;
+import beast.base.spec.type.*;
import beastfx.app.util.FXUtils;
import javafx.scene.Node;
import javafx.scene.control.Button;
@@ -42,6 +20,10 @@
import javafx.scene.layout.Pane;
import javafx.scene.layout.VBox;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
public class TensorDistributionInputEditor extends BEASTObjectInputEditor implements HasExpandBox {
public TensorDistributionInputEditor() {
@@ -420,6 +402,16 @@ private String getParameters() {
b.append(',');
b.append(p.getInput("value").get().toString().trim());
}
+ } else if (o != null && o instanceof RealVectorParam || o instanceof IntVectorParam || o instanceof BoolVectorParam) {
+ // vector hyperparameters (e.g. alpha of Dirichlet)
+ BEASTInterface p = (BEASTInterface) o;
+ if (b == null) {
+ b = new StringBuilder();
+ b.append(p.getInput("value").get().toString().trim());
+ } else {
+ b.append(',');
+ b.append(p.getInput("value").get().toString().trim());
+ }
} else if (o != null && o instanceof Double && !input.getName().equals("offset")) {
Double p = (Double) o;
if (b == null) {
diff --git a/beast-fx/src/main/java/beastfx/app/inputeditor/spec/VectorInputEditor.java b/beast-fx/src/main/java/beastfx/app/inputeditor/spec/VectorInputEditor.java
new file mode 100644
index 00000000..7ac3473a
--- /dev/null
+++ b/beast-fx/src/main/java/beastfx/app/inputeditor/spec/VectorInputEditor.java
@@ -0,0 +1,255 @@
+package beastfx.app.inputeditor.spec;
+
+import beast.base.core.BEASTInterface;
+import beast.base.core.Input;
+import beast.base.inference.Operator;
+import beast.base.inference.StateNode;
+import beast.base.spec.inference.distribution.TensorDistribution;
+import beast.base.spec.inference.parameter.BoolVectorParam;
+import beast.base.spec.inference.parameter.IntVectorParam;
+import beast.base.spec.inference.parameter.RealVectorParam;
+import beast.base.spec.type.Vector;
+import beastfx.app.inputeditor.BEASTObjectInputEditor;
+import beastfx.app.inputeditor.BEASTObjectPanel;
+import beastfx.app.inputeditor.BeautiDoc;
+import beastfx.app.util.FXUtils;
+import javafx.geometry.Insets;
+import javafx.scene.control.CheckBox;
+import javafx.scene.control.Tooltip;
+import javafx.scene.layout.HBox;
+import javafx.scene.layout.Pane;
+
+import java.util.List;
+
+/**
+ * InputEditor for spec vector parameters: RealVectorParam, IntVectorParam,
+ * BoolVectorParam (and their subclasses, e.g. SimplexParam).
+ *
+ * Displays all element values in a single space-separated text field, an
+ * isEstimated checkbox, and an edit button for accessing dimension / domain /
+ * key settings via BEASTObjectDialog.
+ *
+ * Handles IntVector and BoolVector via the same text-field pattern, which is
+ * consistent with how ParameterInputEditor handles the legacy Parameter.Base.
+ */
+public class VectorInputEditor extends BEASTObjectInputEditor {
+
+ public CheckBox m_isEstimatedBox;
+
+ public VectorInputEditor() {
+ super();
+ }
+
+ public VectorInputEditor(BeautiDoc doc) {
+ super(doc);
+ }
+
+ @Override
+ public Class type() {
+ return Vector.class;
+ }
+
+ /**
+ * Register all three concrete vector-param base classes.
+ * Subclasses (e.g. SimplexParam extends RealVectorParam) are found
+ * automatically through InputEditorFactory's superclass walk.
+ */
+ @Override
+ public Class[] types() {
+ return new Class[] {
+ RealVectorParam.class,
+ IntVectorParam.class,
+ BoolVectorParam.class,
+ };
+ }
+
+ @Override
+ public void init(Input input, BEASTInterface beastObject, int itemNr,
+ ExpandOption isExpandOption, boolean addButtons) {
+ if ("param".equals(input.getName()) && beastObject instanceof TensorDistribution) {
+ // TensorDistributionInputEditor shows paramInput via the range button; suppress here
+ pane = FXUtils.newHBox();
+ setVisible(false);
+ setManaged(false);
+ return;
+ }
+ super.init(input, beastObject, itemNr, isExpandOption, addButtons);
+ m_beastObject = beastObject;
+ pane.setPadding(new Insets(5));
+ }
+
+ // --- value helpers ---------------------------------------------------
+
+ private Object resolveParam() {
+ if (itemNr < 0) {
+ return m_input.get();
+ }
+ return ((List) m_input.get()).get(itemNr);
+ }
+
+ /** Space-separated string of all element values. */
+ private String valuesToString(Object param) {
+ StringBuilder sb = new StringBuilder();
+ if (param instanceof RealVectorParam rvp) {
+ for (double v : rvp.getValues()) {
+ if (sb.length() > 0) sb.append(' ');
+ sb.append(v);
+ }
+ } else if (param instanceof IntVectorParam ivp) {
+ for (int v : ivp.getValues()) {
+ if (sb.length() > 0) sb.append(' ');
+ sb.append(v);
+ }
+ } else if (param instanceof BoolVectorParam bvp) {
+ for (boolean v : bvp.getValues()) {
+ if (sb.length() > 0) sb.append(' ');
+ sb.append(v);
+ }
+ }
+ return sb.toString();
+ }
+
+ // --- InputEditor.Base overrides -------------------------------------
+
+ @Override
+ protected void setUpEntry() {
+ super.setUpEntry();
+ // wider field: vectors can have many elements
+ m_entry.setPrefWidth(300);
+ m_entry.setMaxWidth(500);
+ }
+
+ @Override
+ protected void initEntry() {
+ Object param = resolveParam();
+ if (param == null) return;
+ m_entry.setText(valuesToString(param));
+ }
+
+ @Override
+ protected void processEntry() {
+ try {
+ Object param = resolveParam();
+ String text = m_entry.getText().trim();
+
+ if (param instanceof RealVectorParam rvp) {
+ String oldValue = valuesToString(rvp);
+ int oldDim = rvp.size();
+ rvp.valuesInput.setValue(text, rvp);
+ rvp.initAndValidate();
+ if (rvp.size() != oldDim) {
+ rvp.setDimension(oldDim);
+ rvp.valuesInput.setValue(oldValue, rvp);
+ rvp.initAndValidate();
+ throw new IllegalArgumentException("Entry caused change in dimension");
+ }
+ } else if (param instanceof IntVectorParam ivp) {
+ String oldValue = valuesToString(ivp);
+ int oldDim = ivp.size();
+ ivp.valuesInput.setValue(text, ivp);
+ ivp.initAndValidate();
+ if (ivp.size() != oldDim) {
+ ivp.setDimension(oldDim);
+ ivp.valuesInput.setValue(oldValue, ivp);
+ ivp.initAndValidate();
+ throw new IllegalArgumentException("Entry caused change in dimension");
+ }
+ } else if (param instanceof BoolVectorParam bvp) {
+ bvp.valuesInput.setValue(text, bvp);
+ bvp.initAndValidate();
+ }
+
+ validateInput();
+ } catch (Exception ex) {
+ if (m_validateLabel != null) {
+ m_validateLabel.setVisible(true);
+ m_validateLabel.setTooltip(new Tooltip(
+ "Parsing error: " + ex.getMessage() +
+ ". Value was left at " + resolveParam() + "."));
+ m_validateLabel.setColor("orange");
+ }
+ repaint();
+ }
+ }
+
+ /**
+ * Replaces the generic BEASTObject combobox with a text field showing
+ * all element values, an isEstimated checkbox, and an edit button.
+ */
+ @Override
+ protected void addComboBox(Pane box, Input input, BEASTInterface beastObject) {
+ Object parameter = (itemNr >= 0)
+ ? ((List) input.get()).get(itemNr)
+ : input.get();
+
+ if (parameter == null) {
+ super.addComboBox(box, input, beastObject);
+ return;
+ }
+
+ HBox paramBox = FXUtils.newHBox();
+
+ setUpEntry();
+ paramBox.getChildren().add(m_entry);
+ FXUtils.createHMCButton(paramBox, m_beastObject, m_input);
+
+ if (m_bAddButtons && BEASTObjectPanel.countInputs(parameter, doc) > 0) {
+ paramBox.getChildren().add(createEditButton(input));
+ }
+
+ if (parameter instanceof StateNode sn) {
+ m_isEstimatedBox = new CheckBox(
+ doc.beautiConfig.getInputLabel(
+ (BEASTInterface) parameter, sn.isEstimatedInput.getName()));
+ m_isEstimatedBox.setId(input.getName() + ".isEstimated");
+ m_isEstimatedBox.setMaxWidth(Double.POSITIVE_INFINITY);
+ box.setMaxWidth(Double.POSITIVE_INFINITY);
+ m_isEstimatedBox.setSelected(sn.isEstimatedInput.get());
+ m_isEstimatedBox.setTooltip(
+ new Tooltip("Estimate value of this parameter in the MCMC chain"));
+ m_isEstimatedBox.setVisible(doc.isExpertMode());
+
+ for (Object output : ((BEASTInterface) parameter).getOutputs()) {
+ if (output instanceof Operator) {
+ m_isEstimatedBox.setVisible(true);
+ break;
+ }
+ }
+
+ m_isEstimatedBox.setOnAction(e -> {
+ try {
+ sn.isEstimatedInput.setValue(m_isEstimatedBox.isSelected(), sn);
+ hardSync();
+ refreshPanel();
+ } catch (Exception ex) {
+ // ignore
+ }
+ });
+
+ paramBox.getChildren().add(m_isEstimatedBox);
+ }
+
+ box.getChildren().add(paramBox);
+ }
+
+ @Override
+ protected void addValidationLabel() {
+ super.addValidationLabel();
+ // hide the edit button when the isEstimated checkbox is hidden
+ if (m_editBEASTObjectButton != null && m_isEstimatedBox != null) {
+ m_editBEASTObjectButton.setVisible(m_isEstimatedBox.isVisible());
+ }
+ }
+
+ @Override
+ protected void refresh() {
+ Object param = resolveParam();
+ if (param != null && m_entry != null) {
+ m_entry.setText(valuesToString(param));
+ }
+ if (m_isEstimatedBox != null && param instanceof StateNode sn) {
+ m_isEstimatedBox.setSelected(sn.isEstimatedInput.get());
+ }
+ repaint();
+ }
+}
diff --git a/beast-fx/src/main/java/module-info.java b/beast-fx/src/main/java/module-info.java
index 4943921c..3f93d324 100644
--- a/beast-fx/src/main/java/module-info.java
+++ b/beast-fx/src/main/java/module-info.java
@@ -104,6 +104,7 @@
beastfx.app.beauti.TreeDistributionInputEditor,
beastfx.app.inputeditor.spec.SiteModelInputEditor,
beastfx.app.inputeditor.spec.ScalarInputEditor,
+ beastfx.app.inputeditor.spec.VectorInputEditor,
beastfx.app.inputeditor.ScalarDistributionInputEditor,
beastfx.app.inputeditor.TensorDistributionInputEditor,
beastfx.app.inputeditor.IIDInputEditor;
diff --git a/beast-fx/src/main/resources/beast.fx/fxtemplates/Standard.xml b/beast-fx/src/main/resources/beast.fx/fxtemplates/Standard.xml
index a1e06ace..1ec479ae 100644
--- a/beast-fx/src/main/resources/beast.fx/fxtemplates/Standard.xml
+++ b/beast-fx/src/main/resources/beast.fx/fxtemplates/Standard.xml
@@ -290,8 +290,8 @@ ClusterTree/clusterType/,
-
-
+
+
@@ -473,7 +473,7 @@ ClusterTree/clusterType/,
-
+
@@ -486,9 +486,9 @@ ClusterTree/clusterType/,
-
+
+
]]>