Migrate to BEAST 2.7 operators

[walterxie]

TODO:

1. AVMNNoperator for frequencies, site and substitution models, and trees;
2. Strict clock UpDownOperator with AVMNNoperators;
3. relax clock ?
4. replace tree scale operator with more efficient BICESPS operators.

[walterxie]

It is very complex. Each AdaptableVarianceMultivariateNormalOperator will map to each beast partition.

The code needs a Map to store the idref of parameters in an AVMN operator, which has be partially implemented in the branch AVMNNoperator. Check TODO in lphybeast.tobeast.operators.DefaultOperatorStrategy

[walterxie]

The proposed implementation is to add AVMNNoperator separately, after adding all default operators but before adding extra operators. So it needs:

1. guess partition from index added in ID, e.g. *_0, *_1, ...
2. link the required operators in the same partition
3. create XML.

Here is the BEAST template for guide:

            <operator id="AVMNOperator.$(n)" spec="beast.base.evolution.operator.kernel.AdaptableVarianceMultivariateNormalOperator" weight="0.1" 
                coefficient="1.0"
                scaleFactor="1"
                beta="0.05"
                initial="800"
                burnin="400"
                every="1" allowNonsense="true">
            	<transformations id="AVMNSumTransform.$(n)" spec="beast.base.inference.operator.kernel.Transform$LogConstrainedSumTransform" sum="1.0">
            		<!-- frequencies -->
            	</transformations>
            	<transformations id="AVMNLogTransform.$(n)" spec="beast.base.inference.operator.kernel.Transform$LogTransform">
             		<!-- site and substitution model parameters -->
            	</transformations>
            	<transformations id="AVMNNoTransform.$(n)" spec="beast.base.inference.operator.kernel.Transform$NoTransform">
             		<!-- tree -->
            	</transformations>
            </operator>

	        <operator id="StrictClockRateScaler.c:$(n)" spec="beast.base.evolution.operator.AdaptableOperatorSampler" weight="1.5">
                <parameter idref="clockRate.c:$(n)"/>
    	        <operator idref="AVMNOperator.$(n)"/>
        	    <operator id='StrictClockRateScalerX.c:$(n)' spec='kernel.BactrianScaleOperator' scaleFactor="0.75" weight="3" parameter='@clockRate.c:$(n)'/>
	        </operator>

        	<operator id="strictClockUpDownOperator.c:$(n)" spec="beast.base.evolution.operator.AdaptableOperatorSampler" weight="1.5">
                <parameter idref="clockRate.c:$(n)"/>
                <tree idref="Tree.t:$(n)"/>
	            <operator idref="AVMNOperator.$(n)"/>
				<operator id='strictClockUpDownOperatorX.c:$(n)' spec='kernel.BactrianUpDownOperator' scaleFactor="0.75" weight="3">
					<up idref="clockRate.c:$(n)"/>
					<down idref="Tree.t:$(n)"/>
				</operator>
    	    </operator>

        	<operator id="proportionInvariantScaler.s:$(n)" spec="beast.base.evolution.operator.AdaptableOperatorSampler" weight="0.05">
                <parameter idref="proportionInvariant.s:$(n)"/>
            	<operator idref="AVMNOperator.$(n)"/>
            	<operator id='proportionInvariantScalerX.s:$(n)' spec='kernel.BactrianScaleOperator' scaleFactor="0.5" weight="0.1" parameter="@proportionInvariant.s:$(n)"/>
        	</operator>

        	<operator id="mutationRateScaler.s:$(n)" spec="beast.base.evolution.operator.AdaptableOperatorSampler" weight="0.05">
                <parameter idref="mutationRate.s:$(n)"/>
            	<operator idref="AVMNOperator.$(n)"/>
	            <operator id='mutationRateScalerX.s:$(n)' spec='kernel.BactrianScaleOperator' scaleFactor="0.5" weight="0.1" parameter="@mutationRate.s:$(n)"/>
        	</operator>

        	<operator id="gammaShapeScaler.s:$(n)" spec="beast.base.evolution.operator.AdaptableOperatorSampler" weight="0.05">
                <parameter idref="gammaShape.s:$(n)"/>
            	<operator idref="AVMNOperator.$(n)"/>
	            <operator id='gammaShapeScalerX.s:$(n)' spec='kernel.BactrianScaleOperator' scaleFactor="0.5" weight="0.1" parameter="@gammaShape.s:$(n)"/>
        	</operator>