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updates bft and constrained tree to default xml
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@jtmccr1
jtmccr1 committed Nov 19, 2024
1 parent e6d89aa commit 8aed018
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Showing 3 changed files with 142 additions and 149 deletions.
52 changes: 25 additions & 27 deletions src/dr/app/beauti/generator/TreeModelGenerator.java
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Original file line number Diff line number Diff line change
Expand Up @@ -95,39 +95,37 @@ void writeConstrainedTreeModel(PartitionTreeModel model, XMLWriter writer) {
new Attribute[] {
new Attribute.Default<>(XMLParser.ID, treeModelName),
}, false);
writer.writeIDref(OldCoalescentSimulatorParser.COALESCENT_TREE, prefix + STARTING_TREE);

writer.writeTag(ConstrainedTreeModelParser.CONSTRAINTS_TREE,false);
writer.writeIDref(NewickParser.NEWICK, prefix + "constraintsTree" );// TODO magic values!
writer.writeCloseTag(ConstrainedTreeModelParser.CONSTRAINTS_TREE);

writer.writeIDref(OldCoalescentSimulatorParser.COALESCENT_TREE, prefix + STARTING_TREE);

writer.writeCloseTag(ConstrainedTreeModel.CONSTRAINED_TREE_MODEL);

writer.writeComment("Parameter proxies for node heights");

writer.writeComment("Parameter proxies for node heights");

writer.writeOpenTag(TreeModelParser.ROOT_HEIGHT);
writer.writeTag(ParameterParser.PARAMETER,
new Attribute.Default<String>(XMLParser.ID, treeModelName + "." + TreeModelParser.ROOT_HEIGHT), true);
writer.writeCloseTag(TreeModelParser.ROOT_HEIGHT);

writer.writeOpenTag(TreeModelParser.NODE_HEIGHTS, new Attribute.Default<String>(TreeModelParser.INTERNAL_NODES, "true"));
writer.writeTag(ParameterParser.PARAMETER,
new Attribute.Default<String>(XMLParser.ID, treeModelName + "." + "internalNodeHeights"), true);
writer.writeCloseTag(TreeModelParser.NODE_HEIGHTS);

writer.writeOpenTag(RootHeightProxyParameter.PARSER.getParserName(),new Attribute.Default<String>(XMLParser.ID, treeModelName + "." + TreeModelParser.ROOT_HEIGHT));
writer.writeIDref(ConstrainedTreeModelParser.CONSTRAINTS_TREE, treeModelName);
writer.writeCloseTag(RootHeightProxyParameter.PARSER.getParserName());

writer.writeOpenTag(NodeHeightProxyParameter.PARSER.getParserName(),
new Attribute[]{
new Attribute.Default<String>(XMLParser.ID, treeModelName + "." + "internalNodeHeights"),
new Attribute.Default<String>(NodeHeightProxyParameter.INCLUDE_ROOT, "false")
});
writer.writeIDref(ConstrainedTreeModelParser.CONSTRAINTS_TREE, treeModelName);

writer.writeCloseTag(NodeHeightProxyParameter.PARSER.getParserName());


writer.writeOpenTag(NodeHeightProxyParameter.PARSER.getParserName(),
new Attribute[]{
new Attribute.Default<String>(XMLParser.ID, treeModelName + "." + "allInternalNodeHeights"),
new Attribute.Default<String>(NodeHeightProxyParameter.INCLUDE_ROOT, "true")
});
writer.writeIDref(ConstrainedTreeModelParser.CONSTRAINTS_TREE, treeModelName);
writer.writeOpenTag(TreeModelParser.NODE_HEIGHTS,
new Attribute[]{
new Attribute.Default<String>(TreeModelParser.INTERNAL_NODES, "true"),
new Attribute.Default<String>(TreeModelParser.ROOT_NODE, "true")
});
writer.writeTag(ParameterParser.PARAMETER,
new Attribute.Default<String>(XMLParser.ID, treeModelName + "." + "allInternalNodeHeights"), true);
writer.writeCloseTag(TreeModelParser.NODE_HEIGHTS);

// Insertion point for leaf sampling (not currently implemented - parser will throw an error)
generateInsertionPoint(ComponentGenerator.InsertionPoint.IN_TREE_MODEL, model, writer);

writer.writeCloseTag(NodeHeightProxyParameter.PARSER.getParserName());
writer.writeCloseTag(ConstrainedTreeModel.CONSTRAINED_TREE_MODEL);


writeTreeModelStatistics(model, writer);
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172 changes: 55 additions & 117 deletions src/dr/evomodelxml/bigfasttree/BigFastTreeModelParser.java
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Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,11 @@
import dr.evolution.util.Date;
import dr.evolution.util.Taxon;
import dr.evomodel.bigfasttree.BigFastTreeModel;
import dr.evomodel.bigfasttree.thorney.RootHeightProxyParameter;
import dr.evomodel.treedatalikelihood.discrete.NodeHeightProxyParameter;
import dr.evomodelxml.tree.TreeModelParser;
import dr.inference.model.Parameter;
import dr.inference.model.ParameterParser;
import dr.xml.*;

import java.util.logging.Logger;
Expand All @@ -41,46 +45,17 @@
*/
public class BigFastTreeModelParser extends AbstractXMLObjectParser {

public static final String ROOT_HEIGHT = "rootHeight";
public static final String LEAF_HEIGHT = "leafHeight";

public static final String NODE_HEIGHTS = "nodeHeights";
public static final String NODE_RATES = "nodeRates";

public static final String ROOT_NODE = "rootNode";
public static final String INTERNAL_NODES = "internalNodes";
public static final String LEAF_NODES = "leafNodes";

public static final String LEAF_HEIGHTS = "leafHeights";

public static final String FIX_HEIGHTS = "fixHeights";
public static final String FIX_TREE = "fixTree";

public static final String TAXON = "taxon";
public static final String NAME = "name";

public BigFastTreeModelParser() {
rules = new XMLSyntaxRule[]{
new ElementRule(Tree.class),
// new ElementRule(ROOT_HEIGHT, Parameter.class, "A parameter definition with id only (cannot be a reference!)", false),
// AttributeRule.newBooleanRule(FIX_HEIGHTS, true),
// AttributeRule.newBooleanRule(FIX_TREE, true),
// new ElementRule(NODE_HEIGHTS,
// new XMLSyntaxRule[]{
// AttributeRule.newBooleanRule(ROOT_NODE, true, "If true the root height is included in the parameter"),
// AttributeRule.newBooleanRule(INTERNAL_NODES, true, "If true the internal node heights (minus the root) are included in the parameter"),
// new ElementRule(Parameter.class, "A parameter definition with id only (cannot be a reference!)")
// }, 1, Integer.MAX_VALUE),
// new ElementRule(LEAF_HEIGHT,
// new XMLSyntaxRule[]{
// AttributeRule.newStringRule(TAXON, false, "The name of the taxon for the leaf"),
// new ElementRule(Parameter.class, "A parameter definition with id only (cannot be a reference!)")
// }, 0, Integer.MAX_VALUE),
// new ElementRule(LEAF_HEIGHTS,
// new XMLSyntaxRule[]{
// new ElementRule(TaxonList.class, "A set of taxa for which leaf heights are required"),
// new ElementRule(Parameter.class, "A compound parameter containing the leaf heights")
// }, true)
new ElementRule(TreeModelParser.ROOT_HEIGHT, Parameter.class, "A parameter definition with id only (cannot be a reference!)", false),
new ElementRule(TreeModelParser.NODE_HEIGHTS,
new XMLSyntaxRule[]{
AttributeRule.newBooleanRule(TreeModelParser.ROOT_NODE, true, "If true the root height is included in the parameter"),
AttributeRule.newBooleanRule(TreeModelParser.INTERNAL_NODES, true, "If true the internal node heights (minus the root) are included in the parameter"),
new ElementRule(Parameter.class, "A parameter definition with id only (cannot be a reference!)")
}, 1, Integer.MAX_VALUE),
};
}

Expand All @@ -94,92 +69,55 @@ public String getParserName() {
public Object parseXMLObject(XMLObject xo) throws XMLParseException {

Tree tree = (Tree) xo.getChild(Tree.class);
boolean fixHeights = xo.getAttribute(FIX_HEIGHTS, false);
boolean fixTree = xo.getAttribute(FIX_TREE, false);
boolean fixHeights = xo.getAttribute(TreeModelParser.FIX_HEIGHTS, false);
boolean fixTree = xo.getAttribute(TreeModelParser.FIX_TREE, false);

BigFastTreeModel treeModel = new BigFastTreeModel(xo.getId(), tree, fixHeights, fixTree);

// Make proxy parameters
RootHeightProxyParameter rootHeightProxyParameter = new RootHeightProxyParameter("Placeholder_Root_Proxy",
treeModel); // id overwritten below
NodeHeightProxyParameter nodeHeightProxyParameter = new NodeHeightProxyParameter("Placeholder_nodeHeight_Proxy",
treeModel, false);
NodeHeightProxyParameter allNodeHeightProxyParameter = new NodeHeightProxyParameter(
"Placeholder_allNodeHeight_Proxy", treeModel, true);
// parse proxy parameters
for (int i = 0; i < xo.getChildCount(); i++) {
if (xo.getChild(i) instanceof XMLObject) {

XMLObject cxo = (XMLObject) xo.getChild(i);

if (cxo.getName().equals(TreeModelParser.ROOT_HEIGHT)) {
ParameterParser.replaceParameter(cxo, rootHeightProxyParameter);
} else if (cxo.getName().equals(TreeModelParser.NODE_HEIGHTS)) {

boolean rootNode = cxo.getAttribute(TreeModelParser.ROOT_NODE, false);
boolean internalNodes = cxo.getAttribute(TreeModelParser.INTERNAL_NODES, false);
boolean leafNodes = cxo.getAttribute(TreeModelParser.LEAF_NODES, false);
if (leafNodes) {
throw new XMLParseException("leafNodes not currently implemented for bft tree");
}
if (!rootNode && !internalNodes) {
throw new XMLParseException(
"internal or internal and rootNode nodes must be selected for the nodeHeights element");
}
if (internalNodes && rootNode) {
ParameterParser.replaceParameter(cxo, allNodeHeightProxyParameter);
} else if (internalNodes && !rootNode) {
ParameterParser.replaceParameter(cxo, nodeHeightProxyParameter);
}
// options for default tree that are not implemented here yet.
}else if(cxo.getName().equals(TreeModelParser.LEAF_HEIGHT) || cxo.getName().equals(TreeModelParser.LEAF_HEIGHTS)) {
throw new XMLParseException("Leaf sampling not implemented for bft trees");
}else if(cxo.getName().equals(TreeModelParser.NODE_RATES) || cxo.getName().equals(TreeModelParser.NODE_TRAITS)|| cxo.getName().equals(TreeModelParser.LEAF_TRAIT)) {
throw new XMLParseException("Leaf sampling not implemented for bft trees");
}
}
}

Logger.getLogger("dr.evomodel").info("\nCreating the big fast tree model, '" + xo.getId() + "'");

// for (int i = 0; i < xo.getChildCount(); i++) {
// if (xo.getChild(i) instanceof XMLObject) {
//
// XMLObject cxo = (XMLObject) xo.getChild(i);
//
// if (cxo.getName().equals(ROOT_HEIGHT)) {
//
// ParameterParser.replaceParameter(cxo, treeModel.getRootHeightParameter());
//
// } else if (cxo.getName().equals(LEAF_HEIGHT)) {
//
// String taxonName;
// if (cxo.hasAttribute(TAXON)) {
// taxonName = cxo.getStringAttribute(TAXON);
// } else {
// throw new XMLParseException("taxa element missing from leafHeight element in treeModel element");
// }
//
// int index = treeModel.getTaxonIndex(taxonName);
// if (index == -1) {
// throw new XMLParseException("taxon " + taxonName + " not found for leafHeight element in treeModel element");
// }
// NodeRef node = treeModel.getExternalNode(index);
//
// Parameter newParameter = treeModel.getLeafHeightParameter(node);
//
// ParameterParser.replaceParameter(cxo, newParameter);
//
// Taxon taxon = treeModel.getTaxon(index);
//
// setUncertaintyBounds(newParameter, taxon);
//
// } else if (cxo.getName().equals(LEAF_HEIGHTS)) {
// // get a set of leaf height parameters out as a compound parameter...
//
// TaxonList taxa = (TaxonList)cxo.getChild(TaxonList.class);
// Parameter offsetParameter = (Parameter)cxo.getChild(Parameter.class);
//
// CompoundParameter leafHeights = new CompoundParameter("leafHeights");
// for (Taxon taxon : taxa) {
// int index = treeModel.getTaxonIndex(taxon);
// if (index == -1) {
// throw new XMLParseException("taxon " + taxon.getId() + " not found for leafHeight element in treeModel element");
// }
// NodeRef node = treeModel.getExternalNode(index);
//
// Parameter newParameter = treeModel.getLeafHeightParameter(node);
//
// leafHeights.addParameter(newParameter);
//
// setUncertaintyBounds(newParameter, taxon);
// }
//
// ParameterParser.replaceParameter(cxo, leafHeights);
//
// } else if (cxo.getName().equals(NODE_HEIGHTS)) {
//
// boolean rootNode = cxo.getAttribute(ROOT_NODE, false);
// boolean internalNodes = cxo.getAttribute(INTERNAL_NODES, false);
// boolean leafNodes = cxo.getAttribute(LEAF_NODES, false);
//
// if (!rootNode && !internalNodes && !leafNodes) {
// throw new XMLParseException("one or more of root, internal or leaf nodes must be selected for the nodeHeights element");
// }
//
// ParameterParser.replaceParameter(cxo, treeModel.createNodeHeightsParameter(rootNode, internalNodes, leafNodes));
//
// } else {
// throw new XMLParseException("illegal child element in " + getParserName() + ": " + cxo.getName());
// }
//
// } else if (xo.getChild(i) instanceof Tree) {
// // do nothing - already handled
// } else {
// throw new XMLParseException("illegal child element in " + getParserName() + ": " + xo.getChildName(i) + " " + xo.getChild(i));
// }
// }

// Logger.getLogger("dr.evomodel").info(" initial tree topology = " + TreeUtils.uniqueNewick(treeModel, treeModel.getRoot()));

Logger.getLogger("dr.evomodel").info(" taxon count = " + treeModel.getExternalNodeCount());
Logger.getLogger("dr.evomodel").info(" tree height = " + treeModel.getNodeHeight(treeModel.getRoot()));
return treeModel;
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