XML is incorrect if data clamping not in the sink of graphical model

[zjzxiaohei]

If data clamping is not in the sink of the graphical model, a new data which is not clamped will be generated in the xml file. And the new one will be used in the xml file.

[walterxie]

If data clamping, the simulated alignment LPhy value will not be processed by ValueToBeast. So, there is no beast object created for the simulated alignment. Then, use getBEASTObject(alignmentValue.getId()), because

BEASTInterface alignmentParam = context.getBEASTObject(alignmentValue);

alignmentParam will be null.