BEAUti panel bugs

[walterxie]

Three bugs. To replicate, import primate-mtDNA.nex (you can use any data as long as estimating frequencies), link clock and tree, then go to the Prior panel first:

1. The view of Dirichlet prior does not look correct:

2. Click "View" menu to "Show initialisation panel", then it will pop out the err message dialog shown below:

3. Click "View" menu to "Show Starting tree panel", then it will show unexpected view like below:

[walterxie]

I also got many following err in the console, which seems to relate to the 2nd bug about "shape":

class beast.base.spec.domain.UnitInterval != class beast.base.spec.domain.Real
java.lang.StringIndexOutOfBoundsException: Range [0, -1) out of bounds for length 0
input shape could not be added.
java.lang.StringIndexOutOfBoundsException: Range [0, -1) out of bounds for length 0
	at java.base/jdk.internal.util.Preconditions$1.apply(Unknown Source)
	at java.base/jdk.internal.util.Preconditions$1.apply(Unknown Source)
	at java.base/jdk.internal.util.Preconditions$4.apply(Unknown Source)
	at java.base/jdk.internal.util.Preconditions$4.apply(Unknown Source)
	at java.base/jdk.internal.util.Preconditions.outOfBounds(Unknown Source)
	at java.base/jdk.internal.util.Preconditions.outOfBoundsCheckFromToIndex(Unknown Source)
	at java.base/jdk.internal.util.Preconditions.checkFromToIndex(Unknown Source)
	at java.base/java.lang.String.checkBoundsBeginEnd(Unknown Source)
	at java.base/java.lang.String.substring(Unknown Source)
	at beast.fx@2.8.0-SNAPSHOT/beastfx.app.inputeditor.IntegerListInputEditor.initEntry(IntegerListInputEditor.java:73)
	at beast.fx@2.8.0-SNAPSHOT/beastfx.app.inputeditor.IntegerListInputEditor.setUpEntry(IntegerListInputEditor.java:192)
	at beast.fx@2.8.0-SNAPSHOT/beastfx.app.inputeditor.IntegerListInputEditor.init(IntegerListInputEditor.java:176)
	at beast.fx@2.8.0-SNAPSHOT/beastfx.app.inputeditor.InputEditorFactory.createInputEditor(InputEditorFactory.java:264)
	at beast.fx@2.8.0-SNAPSHOT/beastfx.app.inputeditor.InputEditorFactory.createInputEditor(InputEditorFactory.java:145)
	at beast.fx@2.8.0-SNAPSHOT/beastfx.app.inputeditor.InputEditorFactory.addInputs(InputEditorFactory.java:112)
	at beast.fx@2.8.0-SNAPSHOT/beastfx.app.inputeditor.ListInputEditor.updateExpandBox(ListInputEditor.java:294)
	at beast.fx@2.8.0-SNAPSHOT/beastfx.app.inputeditor.ListInputEditor.createExpandBox(ListInputEditor.java:279)
	at beast.fx@2.8.0-SNAPSHOT/beastfx.app.inputeditor.ListInputEditor.addSingleItem(ListInputEditor.java:222)
	at beast.fx@2.8.0-SNAPSHOT/beastfx.app.inputeditor.ListInputEditor.init(ListInputEditor.java:130)
	at beast.fx@2.8.0-SNAPSHOT/beastfx.app.beauti.StateNodeListInputEditor.init(StateNodeListInputEditor.java:36)
	at beast.fx@2.8.0-SNAPSHOT/beastfx.app.inputeditor.InputEditorFactory.createInputEditor(InputEditorFactory.java:264)
	at beast.fx@2.8.0-SNAPSHOT/beastfx.app.inputeditor.InputEditorFactory.createInputEditor(InputEditorFactory.java:145)
	at beast.fx@2.8.0-SNAPSHOT/beastfx.app.inputeditor.BeautiPanel.refreshInputPanel(BeautiPanel.java:318)
	at beast.fx@2.8.0-SNAPSHOT/beastfx.app.inputeditor.BeautiPanel.refreshInputPanel(BeautiPanel.java:373)
	at beast.fx@2.8.0-SNAPSHOT/beastfx.app.inputeditor.BeautiPanel.refreshPanel(BeautiPanel.java:284)
	at beast.fx@2.8.0-SNAPSHOT/beastfx.app.beauti.BeautiTabPane.refreshPanel(BeautiTabPane.java:687)
	at beast.fx@2.8.0-SNAPSHOT/beastfx.app.beauti.BeautiTabPane.lambda$main2$0(BeautiTabPane.java:1269)
	at javafx.base/com.sun.javafx.binding.ExpressionHelper$Generic.fireValueChangedEvent(Unknown Source)
	at javafx.base/com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(Unknown Source)
	at javafx.base/javafx.beans.property.ReadOnlyObjectPropertyBase.fireValueChangedEvent(Unknown Source)
	at javafx.base/javafx.beans.property.ReadOnlyObjectWrapper.fireValueChangedEvent(Unknown Source)
	at javafx.base/javafx.beans.property.ObjectPropertyBase.markInvalid(Unknown Source)
	at javafx.base/javafx.beans.property.ObjectPropertyBase.set(Unknown Source)
	at javafx.controls/javafx.scene.control.SelectionModel.setSelectedItem(Unknown Source)
	at javafx.controls/javafx.scene.control.TabPane$TabPaneSelectionModel.select(Unknown Source)
	at javafx.controls/javafx.scene.control.TabPane$TabPaneSelectionModel.select(Unknown Source)
	at javafx.controls/javafx.scene.control.TabPane$TabPaneSelectionModel.select(Unknown Source)
	at javafx.controls/com.sun.javafx.scene.control.behavior.TabPaneBehavior.selectTab(Unknown Source)
	at javafx.controls/javafx.scene.control.skin.TabPaneSkin$TabHeaderSkin$5.handle(Unknown Source)
	at javafx.controls/javafx.scene.control.skin.TabPaneSkin$TabHeaderSkin$5.handle(Unknown Source)
	at javafx.base/com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(Unknown Source)
	at javafx.base/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
	at javafx.base/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
	at javafx.base/com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(Unknown Source)
	at javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
	at javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
	at javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
	at javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
	at javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
	at javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
	at javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
	at javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
	at javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
	at javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
	at javafx.base/com.sun.javafx.event.EventUtil.fireEventImpl(Unknown Source)
	at javafx.base/com.sun.javafx.event.EventUtil.fireEvent(Unknown Source)
	at javafx.base/javafx.event.Event.fireEvent(Unknown Source)
	at javafx.graphics/javafx.scene.Scene$MouseHandler.process(Unknown Source)
	at javafx.graphics/javafx.scene.Scene.processMouseEvent(Unknown Source)
	at javafx.graphics/javafx.scene.Scene$ScenePeerListener.mouseEvent(Unknown Source)
	at javafx.graphics/com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.get(Unknown Source)
	at javafx.graphics/com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.get(Unknown Source)
	at javafx.graphics/com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(Unknown Source)
	at javafx.graphics/com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(Unknown Source)
	at javafx.graphics/com.sun.glass.ui.View.handleMouseEvent(Unknown Source)
	at javafx.graphics/com.sun.glass.ui.View.notifyMouse(Unknown Source)
	at javafx.graphics/com.sun.glass.ui.mac.MacView.notifyMouse(Unknown Source)

[walterxie]

The 3rd bug is caused by :
The blocks for RandomTree in Standard.xml still reference the old deprecated class names. The main block (line 294) was already updated to beast.base.spec.*, but the subtemplates were missed.

Also review the Standard.xml to find ClusterTree has the same problem, and update its to beast.base.spec.evolution.tree.ClusterTree