Starting tree generated with constraints by BEAUti is not correct XML for BEAST

[GoogleCodeExporter]

When using monophyly constraints, BEAUti generates 'constrainedTaxa' elements 
in the 'coalescentTree' tree generator which don't seem to be correctly 
specified:

    <!-- Generate a random starting tree under the coalescent process            -->
    <coalescentTree id="startingTree">
        <constrainedTaxa>
            <taxa idref="taxa"/>
            <tmrca monophyletic="true">
                <taxa idref="untitled1"/>
            </tmrca>
            <tmrca monophyletic="true">
                <taxa idref="untitled2"/>
                <uniformDistributionModel>
                    <lower>10.0</lower>
                    <upper>20.0</upper>
                </uniformDistributionModel>
            </tmrca>
            <tmrca monophyletic="true">
                <taxa idref="untitled3"/>
            </tmrca>
        </constrainedTaxa>
        <constantSize idref="constant"/>
    </coalescentTree>

BEAST complains about the 'tmrca' elements:

Unexpected element in coalescentTree:startingTree:  tmrca in constrainedTaxa, 
tmrca in constrainedTaxa, tmrca in constrainedTaxa

This means the constraints are not being respected.

Original issue reported on code.google.com by ramb...@gmail.com on 22 Sep 2010 at 9:33

[GoogleCodeExporter]

Looking at this more closely, the 'tmrca' elements are being parsed and 
respected but they are not correctly described in the CoalescentSimulatorParser 
so the warnings are being produced. This is not a critical problem.

Original comment by ramb...@gmail.com on 22 Sep 2010 at 9:39

• Added labels: Priority-Medium
• Removed labels: Priority-Critical

[GoogleCodeExporter]

Original comment by dong.w.xie@gmail.com on 11 Oct 2010 at 9:48

• Changed state: Fixed
• Added labels: 1.6.0, BEAST
• Removed labels: 1.6

[GoogleCodeExporter]

Issue 400 has been merged into this issue.

Original comment by dong.w.xie@gmail.com on 1 Mar 2011 at 3:55