From a3922173f0a2a2bb0cbf5fb63bd05d3a4cd54c72 Mon Sep 17 00:00:00 2001 From: jtmccr1 Date: Wed, 10 Jul 2024 16:47:01 -0700 Subject: [PATCH 01/28] initial look at beauti --- examples/1K.thorney.HMC.xml | 3395 +++++++++++++++++ examples/thorney.xml | 3177 +++++++++++++++ .../thorney/ThorneyComponentFactory.java | 5 + .../thorney/ThorneyComponentGenerator.java | 5 + .../thorney/ThorneyComponentOptions.java | 5 + .../thorney/ThorneySubstModelType.java | 5 + src/dr/app/beauti/options/BeautiOptions.java | 14 + .../options/PartitionSubstitutionModel.java | 10 +- .../sitemodelspanel/PartitionModelPanel.java | 8 + 9 files changed, 6622 insertions(+), 2 deletions(-) create mode 100644 examples/1K.thorney.HMC.xml create mode 100644 examples/thorney.xml create mode 100644 src/dr/app/beauti/components/thorney/ThorneyComponentFactory.java create mode 100644 src/dr/app/beauti/components/thorney/ThorneyComponentGenerator.java create mode 100644 src/dr/app/beauti/components/thorney/ThorneyComponentOptions.java create mode 100644 src/dr/app/beauti/components/thorney/ThorneySubstModelType.java diff --git a/examples/1K.thorney.HMC.xml b/examples/1K.thorney.HMC.xml new file mode 100644 index 0000000000..1d53ad70e9 --- /dev/null +++ b/examples/1K.thorney.HMC.xml @@ -0,0 +1,3395 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/src/dr/app/beauti/components/thorney/ThorneyComponentFactory.java b/src/dr/app/beauti/components/thorney/ThorneyComponentFactory.java new file mode 100644 index 0000000000..c4db0d7a3a --- /dev/null +++ b/src/dr/app/beauti/components/thorney/ThorneyComponentFactory.java @@ -0,0 +1,5 @@ +package dr.app.beauti.components.thorney; + +public class ThorneyComponentFactory { + +} diff --git a/src/dr/app/beauti/components/thorney/ThorneyComponentGenerator.java b/src/dr/app/beauti/components/thorney/ThorneyComponentGenerator.java new file mode 100644 index 0000000000..a017c976d2 --- /dev/null +++ b/src/dr/app/beauti/components/thorney/ThorneyComponentGenerator.java @@ -0,0 +1,5 @@ +package dr.app.beauti.components.thorney; + +public class ThorneyComponentGenerator { + +} diff --git a/src/dr/app/beauti/components/thorney/ThorneyComponentOptions.java b/src/dr/app/beauti/components/thorney/ThorneyComponentOptions.java new file mode 100644 index 0000000000..9d35b4ed43 --- /dev/null +++ b/src/dr/app/beauti/components/thorney/ThorneyComponentOptions.java @@ -0,0 +1,5 @@ +package dr.app.beauti.components.thorney; + +public class ThorneyComponentOptions { + +} diff --git a/src/dr/app/beauti/components/thorney/ThorneySubstModelType.java b/src/dr/app/beauti/components/thorney/ThorneySubstModelType.java new file mode 100644 index 0000000000..88c79d04ca --- /dev/null +++ b/src/dr/app/beauti/components/thorney/ThorneySubstModelType.java @@ -0,0 +1,5 @@ +package dr.app.beauti.components.thorney; + +public class ThorneySubstModelType { + +} diff --git a/src/dr/app/beauti/options/BeautiOptions.java b/src/dr/app/beauti/options/BeautiOptions.java index 6c7d55f3cb..d296d8da65 100644 --- a/src/dr/app/beauti/options/BeautiOptions.java +++ b/src/dr/app/beauti/options/BeautiOptions.java @@ -1117,6 +1117,8 @@ public int createPartitionForTree(TreeHolder trees, String partitionName) { dataPartitions.add(partition); selRow = dataPartitions.size() - 1; + + if (partition.getPartitionTreeModel() == null) { PartitionTreeModel treeModel = new PartitionTreeModel(this, partition); PartitionTreePrior partitionTreePrior = new PartitionTreePrior(this, treeModel); @@ -1124,6 +1126,18 @@ public int createPartitionForTree(TreeHolder trees, String partitionName) { partition.setPartitionTreeModel(treeModel);// always use 1st tree treeModel.setEmpiricalTreesFilename(trees.getFileName()); } + if(partition.getPartitionClockModel() == null) { + PartitionClockModel pcm = new PartitionClockModel(this, DEFAULT_NAME, partition, partition.getPartitionTreeModel()); + partition.setPartitionClockModel(pcm); + } + if (partition.getPartitionSubstitutionModel() == null) { + PartitionSubstitutionModel substModel = new PartitionSubstitutionModel(this, partition.getName(), + partition); + partition.setPartitionSubstitutionModel(substModel); + } + + ContinuousComponentOptions comp = (ContinuousComponentOptions) getComponentOptions(ContinuousComponentOptions.class); + comp.createParameters(this); return selRow; } diff --git a/src/dr/app/beauti/options/PartitionSubstitutionModel.java b/src/dr/app/beauti/options/PartitionSubstitutionModel.java index d57e222866..5a1c9cbdc6 100644 --- a/src/dr/app/beauti/options/PartitionSubstitutionModel.java +++ b/src/dr/app/beauti/options/PartitionSubstitutionModel.java @@ -528,7 +528,10 @@ public List selectParameters(List params) { //Do nothing break; - + case DataType.TREE: + //Do nothing + System.out.println("Tree data type in selectParameters"); + break; default: throw new IllegalArgumentException("Unknown data type"); } @@ -773,7 +776,10 @@ public List selectOperators(List operators) { case DataType.DUMMY: //Do nothing break; - + case DataType.TREE: + //Do nothing + System.out.println("Tree data type in selectOperators"); + break; default: throw new IllegalArgumentException("Unknown data type"); diff --git a/src/dr/app/beauti/sitemodelspanel/PartitionModelPanel.java b/src/dr/app/beauti/sitemodelspanel/PartitionModelPanel.java index 4f9dc37ff7..df5085b0e2 100644 --- a/src/dr/app/beauti/sitemodelspanel/PartitionModelPanel.java +++ b/src/dr/app/beauti/sitemodelspanel/PartitionModelPanel.java @@ -547,6 +547,10 @@ public void setOptions() { //Do nothing break; + case DataType.TREE: + //DO all sorts of things I haven't figured out yet + System.out.println("Tree data type!!!!"); + break; default: throw new IllegalArgumentException("Unknown data type"); @@ -723,6 +727,10 @@ private void setupPanel() { //Do nothing break; + case DataType.TREE: + //DO all sorts of things I haven't figured out yet + System.out.println("Tree data type!!!!"); + break; default: throw new IllegalArgumentException("Unknown data type"); From d3686835400647334a4118ec4019af0c3da7f8de Mon Sep 17 00:00:00 2001 From: jtmccr1 Date: Wed, 10 Jul 2024 16:49:59 -0700 Subject: [PATCH 02/28] git ignore for vscode --- .gitignore | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.gitignore b/.gitignore index ebcdd9a3e8..95393bb8fa 100644 --- a/.gitignore +++ b/.gitignore @@ -20,3 +20,5 @@ src/revision.txt *.dmg release/Mac src/revision.txt +.vscode/launch.json +.vscode/settings.json From 236324df4c5c9c9a85154983a51e256833335081 Mon Sep 17 00:00:00 2001 From: jtmccr1 Date: Wed, 10 Jul 2024 16:52:40 -0700 Subject: [PATCH 03/28] unhide thorney options for dev work --- src/dr/app/beauti/treespanel/PartitionTreeModelPanel.java | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/dr/app/beauti/treespanel/PartitionTreeModelPanel.java b/src/dr/app/beauti/treespanel/PartitionTreeModelPanel.java index e315fc1d37..8fafda7b53 100644 --- a/src/dr/app/beauti/treespanel/PartitionTreeModelPanel.java +++ b/src/dr/app/beauti/treespanel/PartitionTreeModelPanel.java @@ -137,9 +137,9 @@ public PartitionTreeModelPanel(final BeautiFrame parent, PartitionTreeModel part userTreeCombo.setEnabled(enabled); userTreeInfo.setEnabled(enabled); -// for (TreeAsDataType treeAsDataType : TreeAsDataType.values()) { -// treeAsDataModelCombo.addItem(treeAsDataType); -// } + for (TreeAsDataType treeAsDataType : TreeAsDataType.values()) { + treeAsDataModelCombo.addItem(treeAsDataType); + } treeAsDataModelCombo.addItem(TreeAsDataType.EMPRICAL_TREES); PanelUtils.setupComponent(treeAsDataModelCombo); treeAsDataModelCombo.addItemListener(ev -> { From 0637872ba225832516a835021527fc6b42a5d318 Mon Sep 17 00:00:00 2001 From: jtmccr1 Date: Thu, 11 Jul 2024 13:11:57 -0500 Subject: [PATCH 04/28] removes treedatapartition from sites and substitution model --- src/dr/app/beauti/options/BeautiOptions.java | 16 ++++++++++------ .../options/PartitionSubstitutionModel.java | 3 +-- .../sitemodelspanel/PartitionModelPanel.java | 5 ++--- 3 files changed, 13 insertions(+), 11 deletions(-) diff --git a/src/dr/app/beauti/options/BeautiOptions.java b/src/dr/app/beauti/options/BeautiOptions.java index d296d8da65..7570ebd76f 100644 --- a/src/dr/app/beauti/options/BeautiOptions.java +++ b/src/dr/app/beauti/options/BeautiOptions.java @@ -254,7 +254,11 @@ public List selectParameters(List parameters) { Set substitutionModels = new LinkedHashSet(); for (AbstractPartitionData partition : getDataPartitions()) { if (partition.getPartitionClockModel() == model) { - substitutionModels.add(partition.getPartitionSubstitutionModel()); + PartitionSubstitutionModel substitutionModel = partition.getPartitionSubstitutionModel(); + if(substitutionModel!=null){ + substitutionModels.add(substitutionModel); + } + // Tree data doesn't have subsitution model at this point } } @@ -1130,11 +1134,11 @@ public int createPartitionForTree(TreeHolder trees, String partitionName) { PartitionClockModel pcm = new PartitionClockModel(this, DEFAULT_NAME, partition, partition.getPartitionTreeModel()); partition.setPartitionClockModel(pcm); } - if (partition.getPartitionSubstitutionModel() == null) { - PartitionSubstitutionModel substModel = new PartitionSubstitutionModel(this, partition.getName(), - partition); - partition.setPartitionSubstitutionModel(substModel); - } + // if (partition.getPartitionSubstitutionModel() == null) { + // PartitionSubstitutionModel substModel = new PartitionSubstitutionModel(this, partition.getName(), + // partition); + // partition.setPartitionSubstitutionModel(substModel); + // } ContinuousComponentOptions comp = (ContinuousComponentOptions) getComponentOptions(ContinuousComponentOptions.class); comp.createParameters(this); diff --git a/src/dr/app/beauti/options/PartitionSubstitutionModel.java b/src/dr/app/beauti/options/PartitionSubstitutionModel.java index 5a1c9cbdc6..1b2b08a7fe 100644 --- a/src/dr/app/beauti/options/PartitionSubstitutionModel.java +++ b/src/dr/app/beauti/options/PartitionSubstitutionModel.java @@ -530,7 +530,6 @@ public List selectParameters(List params) { case DataType.TREE: //Do nothing - System.out.println("Tree data type in selectParameters"); break; default: throw new IllegalArgumentException("Unknown data type"); @@ -778,7 +777,7 @@ public List selectOperators(List operators) { break; case DataType.TREE: //Do nothing - System.out.println("Tree data type in selectOperators"); + // System.out.println("Tree data type ParitionSubstutionModel selectOperators"); break; default: diff --git a/src/dr/app/beauti/sitemodelspanel/PartitionModelPanel.java b/src/dr/app/beauti/sitemodelspanel/PartitionModelPanel.java index df5085b0e2..2b5f576d3b 100644 --- a/src/dr/app/beauti/sitemodelspanel/PartitionModelPanel.java +++ b/src/dr/app/beauti/sitemodelspanel/PartitionModelPanel.java @@ -548,8 +548,7 @@ public void setOptions() { break; case DataType.TREE: - //DO all sorts of things I haven't figured out yet - System.out.println("Tree data type!!!!"); + //Do nothing break; default: @@ -729,7 +728,7 @@ private void setupPanel() { case DataType.TREE: //DO all sorts of things I haven't figured out yet - System.out.println("Tree data type!!!!"); + // System.out.println("Tree data type in PartitionModelPanel setupPanel"); break; default: throw new IllegalArgumentException("Unknown data type"); From ed3bc283822ffea2cc840c39b70160da8db90a75 Mon Sep 17 00:00:00 2001 From: jtmccr1 Date: Thu, 11 Jul 2024 15:50:12 -0500 Subject: [PATCH 05/28] adds thorney operators --- .../beauti/generator/OperatorsGenerator.java | 33 +++++++++++ .../beauti/options/PartitionTreeModel.java | 55 ++++++++++++++++++- .../treespanel/PartitionTreeModelPanel.java | 38 ++++++++++++- src/dr/app/beauti/types/OperatorType.java | 6 +- .../operators/NodeHeightOperatorParser.java | 12 ++-- 5 files changed, 132 insertions(+), 12 deletions(-) diff --git a/src/dr/app/beauti/generator/OperatorsGenerator.java b/src/dr/app/beauti/generator/OperatorsGenerator.java index 79596825ab..733efdb3a9 100644 --- a/src/dr/app/beauti/generator/OperatorsGenerator.java +++ b/src/dr/app/beauti/generator/OperatorsGenerator.java @@ -32,6 +32,8 @@ import dr.app.beauti.types.TreePriorType; import dr.app.beauti.util.XMLWriter; import dr.evolution.datatype.DataType; +import dr.evomodel.arg.ARGModel.Node; +import dr.evomodel.bigfasttree.thorney.ConstrainedTreeModel; import dr.evomodel.operators.BitFlipInSubstitutionModelOperator; import dr.evomodel.operators.EmpiricalTreeDistributionOperator; import dr.evomodel.tree.DefaultTreeModel; @@ -256,6 +258,12 @@ private void writeOperator(Operator operator, XMLWriter writer) { case SHRINKAGE_CLOCK_GIBBS_OPERATOR: writeShrinkageClockGibbsOperator(operator, prefix, writer); break; + case NODE_HEIGHT_OPERATOR_UNIFORM : + writeBFTUniformNodeHeightOperator(operator, prefix, writer); + break; + case NODE_HEIGHT_OPERATOR_ROOT: + writeBFTUniformRootScaleOperator(operator, prefix, writer); + break; default: throw new IllegalArgumentException("Unknown operator type"); } @@ -717,6 +725,31 @@ private void writeEmpiricalTreeSwapOperator(Operator operator, String treeModelP writer.writeCloseTag(EmpiricalTreeDistributionOperator.EMPIRICAL_TREE_DISTRIBUTION_OPERATOR); } + private void writeBFTUniformNodeHeightOperator(Operator operator, String treeModelPrefix, XMLWriter writer) { + writer.writeOpenTag(NodeHeightOperatorParser.NODE_HEIGHT_OPERATOR, // should this be in the class and not the parser? + new Attribute[]{ + new Attribute.Default("type",NodeHeightOperatorParser.OperatorType.UNIFORM.toString()), + getWeightAttribute(operator.getWeight()) + } + ); + writer.writeIDref(ConstrainedTreeModel.CONSTRAINED_TREE_MODEL, treeModelPrefix + DefaultTreeModel.TREE_MODEL); + writer.writeCloseTag(NodeHeightOperatorParser.NODE_HEIGHT_OPERATOR); + } + + private void writeBFTUniformRootScaleOperator(Operator operator, String treeModelPrefix, XMLWriter writer) { + writer.writeOpenTag(NodeHeightOperatorParser.NODE_HEIGHT_OPERATOR, // should this be in the class and not the parser? + new Attribute[]{ + new Attribute.Default("type",NodeHeightOperatorParser.OperatorType.SCALEROOT.toString()), + // todo scale factor here + new Attribute.Default(NodeHeightOperatorParser.SCALE_FACTOR, operator.getTuning()), + getWeightAttribute(operator.getWeight()) + } + ); + writer.writeIDref(ConstrainedTreeModel.CONSTRAINED_TREE_MODEL, treeModelPrefix + DefaultTreeModel.TREE_MODEL); + writer.writeCloseTag(NodeHeightOperatorParser.NODE_HEIGHT_OPERATOR); + } + + // tuneable version of FHSPR but not currently being used private void writeSubtreeJumpOperator(Operator operator, String treeModelPrefix, XMLWriter writer) { writer.writeOpenTag(SubtreeJumpOperatorParser.SUBTREE_JUMP, diff --git a/src/dr/app/beauti/options/PartitionTreeModel.java b/src/dr/app/beauti/options/PartitionTreeModel.java index 98f8732ce3..2b37359506 100644 --- a/src/dr/app/beauti/options/PartitionTreeModel.java +++ b/src/dr/app/beauti/options/PartitionTreeModel.java @@ -52,11 +52,14 @@ public class PartitionTreeModel extends PartitionOptions { private boolean isUsingExternalEmpiricalTreeFile = false; private String empiricalTreesFilename = null; + private int thorneyScaler = 1; private boolean isNewick = true; private boolean hasTipCalibrations = false; private boolean hasNodeCalibrations = false; + + private final TreePartitionData treePartitionData; public PartitionTreeModel(BeautiOptions options, String name) { @@ -102,6 +105,9 @@ public PartitionTreeModel(BeautiOptions options, String name, PartitionTreeModel public void initModelParametersAndOpererators() { + + + createParameter("tree", "The tree"); createParameter("treeModel.internalNodeHeights", "internal node heights of the tree (except the root)"); createParameter("treeModel.allInternalNodeHeights", "internal node heights of the tree"); @@ -136,13 +142,33 @@ public void initModelParametersAndOpererators() { createOperator("FHSPR", "Tree", "Performs the fixed-height subtree prune/regraft of the tree", "tree", OperatorType.FIXED_HEIGHT_SUBTREE_PRUNE_REGRAFT, 1.0, weight); } else { + //Thorney BEAST operators here? double weight = Math.max(options.taxonList.getTaxonCount(), 30); + + // does STL works on constrained trees? createOperator("subtreeLeap", "Tree", "Performs the subtree-leap rearrangement of the tree", "tree", OperatorType.SUBTREE_LEAP, 1.0, weight); - weight = Math.max(weight / 10, 3); + createOperator("nodeHeight-uniform","Tree", "Draws new internal node heights on constrained tree uniformally","tree", + OperatorType.NODE_HEIGHT_OPERATOR_UNIFORM,-1.0, treeWeights); + + // In the TB setting this will almost always give the same likelihood since coalescent doesn't change + // and if we are in the non mutation zone the treelikelihood will be the same. createOperator("FHSPR", "Tree", "Performs the fixed-height subtree prune/regraft of the tree", "tree", OperatorType.FIXED_HEIGHT_SUBTREE_PRUNE_REGRAFT, 1.0, weight); + createOperator("narrowExchange", "Tree", "Performs local rearrangements of the tree", "tree", + OperatorType.NARROW_EXCHANGE, -1, weight); + createOperator("wideExchange", "Tree", "Performs global rearrangements of the tree", "tree", + OperatorType.WIDE_EXCHANGE, -1, weight); + + weight = Math.max(weight / 10, 3); + + // these work on bft tree models + createOperator("nodeHeight-root","Tree", "Draws new root height on constrained tree","tree", + OperatorType.NODE_HEIGHT_OPERATOR_ROOT,demoTuning, weight); + + createOperator("wilsonBalding", "Tree", "Performs the Wilson-Balding rearrangement of the tree", "tree", + OperatorType.WILSON_BALDING, -1, weight); } createOperator("empiricalTreeSwap", "Tree", "Sets the current tree from the empirical set", "tree", @@ -155,7 +181,11 @@ public List selectParameters(List parameters) { // Don't add these to the parameter list (as they don't appear in the table), but call // get parameter so their id prefix can be set. + getParameter("tree"); + if(isUsingEmpiricalTrees()||isUsingThorneyBEAST()){ + return parameters; + } getParameter("treeModel.internalNodeHeights"); getParameter("treeModel.allInternalNodeHeights"); @@ -179,7 +209,18 @@ public List selectOperators(List operators) { if (isUsingEmpiricalTrees()) { operators.add(getOperator("empiricalTreeSwap")); - } else { + } else if(isUsingThorneyBEAST()){ + operators.add(getOperator("narrowExchange")); + operators.add(getOperator("wideExchange")); + operators.add(getOperator("wilsonBalding")); + + operators.add(getOperator("FHSPR")); + + operators.add(getOperator("nodeHeight-uniform")); + operators.add(getOperator("nodeHeight-root")); + + + }else { if (treePartitionData == null) { Operator subtreeSlideOp = getOperator("subtreeSlide"); if (!subtreeSlideOp.isTuningEdited()) { @@ -283,6 +324,9 @@ public boolean isUsingEmpiricalTrees() { return treePartitionData != null && treeAsDataType == TreeAsDataType.EMPRICAL_TREES; } + public boolean isUsingThorneyBEAST(){ + return treePartitionData != null && treeAsDataType == TreeAsDataType.THORNEY_BEAST; + } public void setUsingExternalEmpiricalTreeFile(boolean isUsingExternalEmpiricalTreeFile) { this.isUsingExternalEmpiricalTreeFile = isUsingExternalEmpiricalTreeFile; } @@ -301,6 +345,13 @@ public void setEmpiricalTreesFilename(String empiricalTreesFilename) { this.empiricalTreesFilename = empiricalTreesFilename; } + public int getThorneyScaler() { + return thorneyScaler; + } + public void setThorneyScaler(int scaler){ + this.thorneyScaler = scaler;; + } + public void setTipCalibrations(boolean hasTipCalibrations) { this.hasTipCalibrations = hasTipCalibrations; } diff --git a/src/dr/app/beauti/treespanel/PartitionTreeModelPanel.java b/src/dr/app/beauti/treespanel/PartitionTreeModelPanel.java index 8fafda7b53..f67eaba23d 100644 --- a/src/dr/app/beauti/treespanel/PartitionTreeModelPanel.java +++ b/src/dr/app/beauti/treespanel/PartitionTreeModelPanel.java @@ -37,6 +37,7 @@ import dr.app.beauti.util.BEAUTiImporter; import dr.app.beauti.util.PanelUtils; import dr.app.gui.components.RealNumberField; +import dr.app.gui.components.WholeNumberField; import dr.app.util.OSType; import dr.evolution.datatype.DataType; import dr.evolution.tree.NodeRef; @@ -79,13 +80,16 @@ public class PartitionTreeModelPanel extends OptionsPanel { private JComboBox treeAsDataModelCombo = new JComboBox(); + private WholeNumberField thorneyGenomeLength = new WholeNumberField(1, Integer.MAX_VALUE); private final OptionsPanel thorneyBEASTPanel; private final JLabel thorneyBEASTInfo = new JLabel("" + "Use the tree and branch lengths in substitutions per site as data, integrating over unresolved
" + - "polytomies and sampling branch lengths.

" + - "Citation: du Plessis L, McCrone JT, et al. (2021) Establishment and lineage dynamics of the SARS-CoV-2 epidemic
" + - "in the UK. Science 371, 708-712. DOI:10.1126/science.abf2946"); + "polytomies and sampling branch lengths.

"); + + private final JLabel thorneyBEASTCitation = new JLabel(""+ + "Citation: du Plessis L, McCrone JT, et al. (2021) Establishment and lineage dynamics of the SARS-CoV-2 epidemic
" + + "in the UK. Science 371, 708-712. DOI:10.1126/science.abf2946 "); private final OptionsPanel empiricalTreePanel; private final JLabel empiricalTreeLabel = new JLabel("Trees filename:"); @@ -173,6 +177,27 @@ public PartitionTreeModelPanel(final BeautiFrame parent, PartitionTreeModel part thorneyBEASTPanel = new OptionsPanel(); thorneyBEASTPanel.setOpaque(false); + PanelUtils.setupComponent(thorneyGenomeLength); + + thorneyGenomeLength.setToolTipText("" + + "This scales branches in the input tree
" + + "to represent expected number of mutations in the genome.
" + + "It should likely be the length of the alignment to used to build the tree."); + thorneyGenomeLength.addKeyListener(new java.awt.event.KeyAdapter() { + public void keyTyped(KeyEvent e) { + } + + public void keyPressed(KeyEvent e) { + } + + public void keyReleased(KeyEvent e) { + PartitionTreeModelPanel.this.partitionTreeModel.setThorneyScaler(thorneyGenomeLength.getValue()); + parent.setDirty(); + } + }); + thorneyGenomeLength.setColumns(10); + + PanelUtils.setupComponent(empiricalExternalFileCheck); empiricalExternalFileCheck.addActionListener(ev -> { empiricalTreeInfo.setEnabled(empiricalExternalFileCheck.isSelected()); @@ -252,6 +277,8 @@ public void setupPanel() { thorneyBEASTPanel.removeAll(); thorneyBEASTPanel.addComponent(thorneyBEASTInfo); + thorneyBEASTPanel.addComponentWithLabel("Scaler", thorneyGenomeLength); + thorneyBEASTPanel.addComponent(thorneyBEASTCitation); empiricalTreePanel.removeAll(); empiricalTreePanel.addComponent(new JLabel( "Use the loaded trees as an empirical set to sample over.")); @@ -305,6 +332,11 @@ public void setOptions() { treeAsDataModelCombo.setSelectedItem(partitionTreeModel.getTreeAsDataType()); empiricalExternalFileCheck.setSelected(partitionTreeModel.isUsingExternalEmpiricalTreeFile()); empiricalFilenameField.setText(partitionTreeModel.getEmpiricalTreesFilename()); + + + thorneyGenomeLength.setValue(partitionTreeModel.getThorneyScaler()); + + } public void getOptions(BeautiOptions options) { diff --git a/src/dr/app/beauti/types/OperatorType.java b/src/dr/app/beauti/types/OperatorType.java index c5afbe514b..0b68c75ba1 100644 --- a/src/dr/app/beauti/types/OperatorType.java +++ b/src/dr/app/beauti/types/OperatorType.java @@ -73,7 +73,11 @@ public enum OperatorType { WILSON_BALDING("wilsonBalding"), RELAXED_CLOCK_HMC_OPERATOR("relaxedClockHMCOperator"), SHRINKAGE_CLOCK_HMC_OPERATOR("shrinkageClockHMCOperator"), - SHRINKAGE_CLOCK_GIBBS_OPERATOR("relaxedClockGibbsOperator"); + SHRINKAGE_CLOCK_GIBBS_OPERATOR("relaxedClockGibbsOperator"), + + //BFT operators + NODE_HEIGHT_OPERATOR_UNIFORM("nodeHeightOperator-uniform"), + NODE_HEIGHT_OPERATOR_ROOT("nodeHeightOperator-scaleRoot"); OperatorType(String displayName) { this.displayName = displayName; diff --git a/src/dr/evomodelxml/operators/NodeHeightOperatorParser.java b/src/dr/evomodelxml/operators/NodeHeightOperatorParser.java index 48b7667165..0618ef2072 100644 --- a/src/dr/evomodelxml/operators/NodeHeightOperatorParser.java +++ b/src/dr/evomodelxml/operators/NodeHeightOperatorParser.java @@ -107,12 +107,12 @@ public Object parseXMLObject(XMLObject xo) throws XMLParseException { throw new XMLParseException("The UniformNodeHeightOperator scaleFactor attribute must be between 0 and 1."); } } - if (xo.hasAttribute(MEAN_COUNT)) { - tuningParameter = xo.getDoubleAttribute(MEAN_COUNT); - if (tuningParameter <= 0.0) { - throw new XMLParseException("The UniformNodeHeightOperator nonshifted mean attribute must be positive and non-zero."); - } - } + // if (xo.hasAttribute(MEAN_COUNT)) { + // tuningParameter = xo.getDoubleAttribute(MEAN_COUNT); + // if (tuningParameter <= 0.0) { + // throw new XMLParseException("The UniformNodeHeightOperator nonshifted mean attribute must be positive and non-zero."); + // } + // } final double targetAcceptance = xo.getAttribute(TARGET_ACCEPTANCE, 0.234); From b22eb1fac2902f95ab237aaf851abb3fa0d7c60a Mon Sep 17 00:00:00 2001 From: jtmccr1 Date: Thu, 11 Jul 2024 16:37:36 -0500 Subject: [PATCH 06/28] Adds initial tree --- .../generator/InitialTreeGenerator.java | 34 +++++++++++++++- .../beauti/generator/TreeModelGenerator.java | 39 +++++++++++++++++-- 2 files changed, 68 insertions(+), 5 deletions(-) diff --git a/src/dr/app/beauti/generator/InitialTreeGenerator.java b/src/dr/app/beauti/generator/InitialTreeGenerator.java index afa190e553..7de49458bc 100644 --- a/src/dr/app/beauti/generator/InitialTreeGenerator.java +++ b/src/dr/app/beauti/generator/InitialTreeGenerator.java @@ -107,8 +107,39 @@ public void writeStartingTree(PartitionTreeModel model, XMLWriter writer) { break; case RANDOM: - // generate a coalescent tree String simulatorId = prefix + STARTING_TREE; + String constraintID = prefix + "constraintsTree"; + if(model.isUsingThorneyBEAST()){ + // write tree with dates + writer.writeComment("The user-specified tree with dates used to simualte a compatible bifurcating starting tree."); + writer.writeOpenTag( + NewickParser.NEWICK, + new Attribute[]{ + new Attribute.Default<>(XMLParser.ID, constraintID), + new Attribute.Default(SimpleTreeParser.USING_DATES, options.useTipDates) + } + ); + writer.writeText(TreeUtils.newick(model.getTreePartitionData().getTrees().getTrees().get(0))); + writer.writeCloseTag(NewickParser.NEWICK); + + writer.writeComment("Generate a random starting tree under the coalescent process"); + writer.writeOpenTag( + CoalescentSimulatorParser.COALESCENT_SIMULATOR, + new Attribute[]{ + new Attribute.Default(XMLParser.ID, simulatorId) + }); + writeInitialDemoModelRef(model, writer); + writer.writeTag( + CoalescentSimulatorParser.CONSTRAINTS_TREE, + false + ); + writer.writeIDref(NewickParser.NEWICK, constraintID); + writer.writeCloseTag(CoalescentSimulatorParser.CONSTRAINTS_TREE); + writer.writeCloseTag(CoalescentSimulatorParser.COALESCENT_SIMULATOR); + + }else{ + + // generate a coalescent tree String taxaId = TaxaParser.TAXA; AbstractPartitionData partition = options.getDataPartitions(model).get(0); @@ -135,6 +166,7 @@ public void writeStartingTree(PartitionTreeModel model, XMLWriter writer) { writeInitialDemoModelRef(model, writer); writer.writeCloseTag(CoalescentSimulatorParser.COALESCENT_SIMULATOR); } + } break; default: diff --git a/src/dr/app/beauti/generator/TreeModelGenerator.java b/src/dr/app/beauti/generator/TreeModelGenerator.java index e7293a4e1c..8ac197f708 100644 --- a/src/dr/app/beauti/generator/TreeModelGenerator.java +++ b/src/dr/app/beauti/generator/TreeModelGenerator.java @@ -31,10 +31,13 @@ import dr.app.beauti.options.BeautiOptions; import dr.app.beauti.options.PartitionTreeModel; import dr.app.beauti.util.XMLWriter; +import dr.evomodel.bigfasttree.thorney.ConstrainedTreeModel; import dr.evomodel.tree.DefaultTreeModel; import dr.evomodel.tree.EmpiricalTreeDistributionModel; +import dr.evomodelxml.bigfasttree.thorney.ConstrainedTreeModelParser; import dr.evomodelxml.coalescent.OldCoalescentSimulatorParser; import dr.evomodelxml.tree.*; +import dr.evoxml.NewickParser; import dr.evoxml.TaxaParser; import dr.evoxml.UPGMATreeParser; import dr.inference.model.ParameterParser; @@ -56,13 +59,14 @@ public TreeModelGenerator(BeautiOptions options, ComponentFactory[] components) void writeTreeModel(PartitionTreeModel model, XMLWriter writer) { if (model.isUsingEmpiricalTrees()) { - writeEmpiricalTreeModel(model, writer); - } else { + writeEmpiricalTreeModel(model, writer); + } else if(model.isUsingThorneyBEAST()){ + writeConstrainedTreeModel(model, writer); + } + else { writeDefaultTreeModel(model, writer); } - //if ThorneyBEAST - //writeConstrainedTreeModel(model, writer); } /** @@ -71,7 +75,34 @@ void writeTreeModel(PartitionTreeModel model, XMLWriter writer) { * @param model * @param writer the writer */ + + void writeConstrainedTreeModel(PartitionTreeModel model, XMLWriter writer) { + // write newick with dates + //simulate tree + //write tree model + + String prefix = model.getPrefix(); + + final String treeModelName = prefix + DefaultTreeModel.TREE_MODEL; // treemodel.treeModel or treeModel + final String STARTING_TREE = InitialTreeGenerator.STARTING_TREE; +// newick written by starting tree + + writer.writeComment("A constrained tree model"); + writer.writeTag(ConstrainedTreeModel.CONSTRAINED_TREE_MODEL, + new Attribute[] { + new Attribute.Default<>(XMLParser.ID, treeModelName), + }, false); + 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); + + + writeTreeModelStatistics(model, writer); } From 183d17e99ad0e69c89ab0b8504dd4dc1da8e7cc9 Mon Sep 17 00:00:00 2001 From: jtmccr1 Date: Thu, 11 Jul 2024 17:14:46 -0500 Subject: [PATCH 07/28] adds likelihood block --- .../generator/TreeLikelihoodGenerator.java | 81 ++++++++++++++++++- .../beauti/options/PartitionTreeModel.java | 8 +- .../treespanel/PartitionTreeModelPanel.java | 2 +- 3 files changed, 84 insertions(+), 7 deletions(-) diff --git a/src/dr/app/beauti/generator/TreeLikelihoodGenerator.java b/src/dr/app/beauti/generator/TreeLikelihoodGenerator.java index 1e6043e71a..0b43eac9c8 100644 --- a/src/dr/app/beauti/generator/TreeLikelihoodGenerator.java +++ b/src/dr/app/beauti/generator/TreeLikelihoodGenerator.java @@ -29,6 +29,9 @@ import dr.app.beauti.types.ClockType; import dr.evomodel.tree.DefaultTreeModel; +import dr.evomodelxml.bigfasttree.thorney.ConstrainedBranchLengthProviderParser; +import dr.evomodelxml.bigfasttree.thorney.PoissonBranchLengthLikelihoodParser; +import dr.evomodelxml.bigfasttree.thorney.ThorneyTreeLikelihoodParser; import dr.evomodelxml.treedatalikelihood.TreeDataLikelihoodParser; import dr.evomodelxml.treelikelihood.MarkovJumpsTreeLikelihoodParser; import dr.app.beauti.components.ComponentFactory; @@ -36,12 +39,19 @@ import dr.app.beauti.options.*; import dr.app.beauti.util.XMLWriter; import dr.evolution.datatype.DataType; +import dr.evolution.tree.TreeUtils; +import dr.evomodel.bigfasttree.thorney.ConstrainedTreeBranchLengthProvider; +import dr.evomodel.bigfasttree.thorney.ConstrainedTreeModel; +import dr.evomodel.bigfasttree.thorney.MutationBranchMap; +import dr.evomodel.bigfasttree.thorney.PoissonBranchLengthLikelihoodDelegate; import dr.evomodel.branchratemodel.BranchRateModel; import dr.oldevomodel.sitemodel.GammaSiteModel; import dr.oldevomodel.sitemodel.SiteModel; import dr.oldevomodelxml.treelikelihood.AncestralStateTreeLikelihoodParser; import dr.oldevomodelxml.treelikelihood.TreeLikelihoodParser; import dr.evoxml.AlignmentParser; +import dr.evoxml.NewickParser; +import dr.evoxml.SimpleTreeParser; import dr.evoxml.SitePatternsParser; import dr.util.Attribute; import dr.xml.XMLParser; @@ -74,13 +84,80 @@ public void writeAllTreeLikelihoods(XMLWriter writer) throws GeneratorException // if the partition isn't an instanceof PartitionData then it doesn't // need a TreeLikelihood (it is probably a Tree Partition) -// } else { -// throw new GeneratorException("Unrecognized partition:\n" + partition.getName()); + } else { + if(partition instanceof TreePartitionData) { + PartitionTreeModel model = partition.getPartitionTreeModel(); + if(model.isUsingThorneyBEAST()){ + writeThorneyTreeLikelihood((TreePartitionData) partition, writer); + writer.writeText(""); + } + + } } } } } + public void writeThorneyTreeLikelihood(TreePartitionData partition,XMLWriter writer){ + // write mutation branch map + +/** + * + + + + + + */ + + PartitionTreeModel treeModel = partition.getPartitionTreeModel(); + PartitionClockModel clockModel = partition.getPartitionClockModel(); + String prefix = treeModel.getPrefix() + clockModel.getPrefix(); // use the treemodel prefix + + String idString = prefix + "treeLikelihood"; + String branchMapIdD = prefix + "branchMutationCounts"; + + + writer.writeComment("A map between the branches in the tree model and the data providing the number of mutations along each branch."); + writer.writeTag(ConstrainedBranchLengthProviderParser.MUTATION_BRANCH_MAP, new Attribute[]{ + new Attribute.Default<>(XMLParser.ID,branchMapIdD), + new Attribute.Default("scale",treeModel.getThorneyScaler()), + },false); + writer.writeIDref(ConstrainedTreeModel.CONSTRAINED_TREE_MODEL, partition.getPrefix() + DefaultTreeModel.TREE_MODEL); + writer.writeTag(ConstrainedBranchLengthProviderParser.DATA_TREE, new Attribute[]{}, false); + writer.writeOpenTag( + NewickParser.NEWICK, + new Attribute[]{ + new Attribute.Default<>(XMLParser.ID, prefix + "dataTree"), + new Attribute.Default(NewickParser.USING_HEIGHTS, true) + } + ); + writer.writeText(TreeUtils.newick(treeModel.getTreePartitionData().getTrees().getTrees().get(0))); + writer.writeCloseTag(NewickParser.NEWICK); + writer.writeCloseTag(ConstrainedBranchLengthProviderParser.DATA_TREE); + writer.writeCloseTag(ConstrainedBranchLengthProviderParser.MUTATION_BRANCH_MAP); + + + + writer.writeOpenTag(ThorneyTreeLikelihoodParser.THORNEY_DATA_LIKELIHOOD_DELEGATE, new Attribute[]{ + new Attribute.Default(XMLParser.ID, idString) + }); + + writer.writeIDref(ConstrainedTreeModel.CONSTRAINED_TREE_MODEL, partition.getPrefix() + DefaultTreeModel.TREE_MODEL); + writer.writeIDref(ConstrainedBranchLengthProviderParser.MUTATION_BRANCH_MAP, branchMapIdD ); + + + writer.writeTag( PoissonBranchLengthLikelihoodParser.POISSON_BRANCH_LENGTH_LIKELIHOOD, + new Attribute[] { + new Attribute.Default<>(XMLParser.ID, prefix + "branchMutationLikelihood"), + new Attribute.Default("scale", treeModel.getThorneyScaler()), + }, true); + + ClockModelGenerator.writeBranchRatesModelRef(clockModel, writer); + + writer.writeCloseTag(ThorneyTreeLikelihoodParser.THORNEY_DATA_LIKELIHOOD_DELEGATE); + } + public void writeTreeDataLikelihood(List partitions, XMLWriter writer) { PartitionSubstitutionModel substModel = partitions.get(0).getPartitionSubstitutionModel(); diff --git a/src/dr/app/beauti/options/PartitionTreeModel.java b/src/dr/app/beauti/options/PartitionTreeModel.java index 2b37359506..4517cac9b0 100644 --- a/src/dr/app/beauti/options/PartitionTreeModel.java +++ b/src/dr/app/beauti/options/PartitionTreeModel.java @@ -52,7 +52,7 @@ public class PartitionTreeModel extends PartitionOptions { private boolean isUsingExternalEmpiricalTreeFile = false; private String empiricalTreesFilename = null; - private int thorneyScaler = 1; + private double thorneyScaler = 1.0; private boolean isNewick = true; private boolean hasTipCalibrations = false; @@ -345,11 +345,11 @@ public void setEmpiricalTreesFilename(String empiricalTreesFilename) { this.empiricalTreesFilename = empiricalTreesFilename; } - public int getThorneyScaler() { + public double getThorneyScaler() { return thorneyScaler; } - public void setThorneyScaler(int scaler){ - this.thorneyScaler = scaler;; + public void setThorneyScaler(double scaler){ + this.thorneyScaler = scaler; } public void setTipCalibrations(boolean hasTipCalibrations) { diff --git a/src/dr/app/beauti/treespanel/PartitionTreeModelPanel.java b/src/dr/app/beauti/treespanel/PartitionTreeModelPanel.java index f67eaba23d..42bd51aae1 100644 --- a/src/dr/app/beauti/treespanel/PartitionTreeModelPanel.java +++ b/src/dr/app/beauti/treespanel/PartitionTreeModelPanel.java @@ -80,7 +80,7 @@ public class PartitionTreeModelPanel extends OptionsPanel { private JComboBox treeAsDataModelCombo = new JComboBox(); - private WholeNumberField thorneyGenomeLength = new WholeNumberField(1, Integer.MAX_VALUE); + private RealNumberField thorneyGenomeLength = new RealNumberField(1.0, Double.MAX_VALUE); private final OptionsPanel thorneyBEASTPanel; private final JLabel thorneyBEASTInfo = new JLabel("" + From d2d768f32e60a6a2f4f86f168aeb7b12f128cbce Mon Sep 17 00:00:00 2001 From: jtmccr1 Date: Thu, 11 Jul 2024 21:39:09 -0500 Subject: [PATCH 08/28] fixes bug in treemodel idref --- .../generator/TreeLikelihoodGenerator.java | 17 ++++++++++++++--- 1 file changed, 14 insertions(+), 3 deletions(-) diff --git a/src/dr/app/beauti/generator/TreeLikelihoodGenerator.java b/src/dr/app/beauti/generator/TreeLikelihoodGenerator.java index 0b43eac9c8..94cfb68dd6 100644 --- a/src/dr/app/beauti/generator/TreeLikelihoodGenerator.java +++ b/src/dr/app/beauti/generator/TreeLikelihoodGenerator.java @@ -123,13 +123,14 @@ public void writeThorneyTreeLikelihood(TreePartitionData partition,XMLWriter wri new Attribute.Default<>(XMLParser.ID,branchMapIdD), new Attribute.Default("scale",treeModel.getThorneyScaler()), },false); - writer.writeIDref(ConstrainedTreeModel.CONSTRAINED_TREE_MODEL, partition.getPrefix() + DefaultTreeModel.TREE_MODEL); + writer.writeIDref(ConstrainedTreeModel.CONSTRAINED_TREE_MODEL,prefix+ DefaultTreeModel.TREE_MODEL); writer.writeTag(ConstrainedBranchLengthProviderParser.DATA_TREE, new Attribute[]{}, false); writer.writeOpenTag( NewickParser.NEWICK, new Attribute[]{ new Attribute.Default<>(XMLParser.ID, prefix + "dataTree"), - new Attribute.Default(NewickParser.USING_HEIGHTS, true) + new Attribute.Default(NewickParser.USING_HEIGHTS, true), + new Attribute.Default(NewickParser.USING_DATES, false) } ); writer.writeText(TreeUtils.newick(treeModel.getTreePartitionData().getTrees().getTrees().get(0))); @@ -143,7 +144,7 @@ public void writeThorneyTreeLikelihood(TreePartitionData partition,XMLWriter wri new Attribute.Default(XMLParser.ID, idString) }); - writer.writeIDref(ConstrainedTreeModel.CONSTRAINED_TREE_MODEL, partition.getPrefix() + DefaultTreeModel.TREE_MODEL); + writer.writeIDref(ConstrainedTreeModel.CONSTRAINED_TREE_MODEL, prefix + DefaultTreeModel.TREE_MODEL); writer.writeIDref(ConstrainedBranchLengthProviderParser.MUTATION_BRANCH_MAP, branchMapIdD ); @@ -364,6 +365,16 @@ public void writeTreeLikelihoodReferences(XMLWriter writer) { AncestralStatesComponentOptions ancestralStatesOptions = (AncestralStatesComponentOptions) options .getComponentOptions(AncestralStatesComponentOptions.class); + // TODO moving poisson branch length to a substitution model would make this logic simplier + + PartitionTreeModel treeModel = partition.getPartitionTreeModel(); + if(treeModel.isUsingThorneyBEAST()){ + PartitionClockModel clockModel = partition.getPartitionClockModel(); + String prefix = treeModel.getPrefix() + clockModel.getPrefix(); // use the treemodel prefix + String idString = prefix + "treeLikelihood"; // Line 117 + writer.writeIDref(ThorneyTreeLikelihoodParser.THORNEY_DATA_LIKELIHOOD_DELEGATE, idString); + + } PartitionSubstitutionModel model = partition.getPartitionSubstitutionModel(); if (model == null) { From b952961482f7c70057620ad5a3ed59d1014ba665 Mon Sep 17 00:00:00 2001 From: jtmccr1 Date: Thu, 11 Jul 2024 21:39:49 -0500 Subject: [PATCH 09/28] operator work --- .../beauti/generator/OperatorsGenerator.java | 21 ++++++++++++--- .../beauti/options/PartitionTreeModel.java | 26 +++++++++++++------ src/dr/app/beauti/types/OperatorType.java | 1 + .../operators/NodeHeightOperatorParser.java | 4 +-- 4 files changed, 38 insertions(+), 14 deletions(-) diff --git a/src/dr/app/beauti/generator/OperatorsGenerator.java b/src/dr/app/beauti/generator/OperatorsGenerator.java index 733efdb3a9..3ede023d23 100644 --- a/src/dr/app/beauti/generator/OperatorsGenerator.java +++ b/src/dr/app/beauti/generator/OperatorsGenerator.java @@ -40,6 +40,7 @@ import dr.evomodel.tree.EmpiricalTreeDistributionModel; import dr.evomodel.treedatalikelihood.TreeDataLikelihood; import dr.evomodel.treedatalikelihood.continuous.BranchRateGradient; +import dr.evomodelxml.bigfasttree.thorney.UniformSubtreePruneRegraftParser; import dr.evomodelxml.branchratemodel.AutoCorrelatedBranchRatesDistributionParser; import dr.evomodelxml.branchratemodel.AutoCorrelatedGradientWrtIncrementsParser; import dr.evomodelxml.branchratemodel.BranchRateGradientWrtIncrementsParser; @@ -260,10 +261,13 @@ private void writeOperator(Operator operator, XMLWriter writer) { break; case NODE_HEIGHT_OPERATOR_UNIFORM : writeBFTUniformNodeHeightOperator(operator, prefix, writer); - break; + break; case NODE_HEIGHT_OPERATOR_ROOT: - writeBFTUniformRootScaleOperator(operator, prefix, writer); - break; + writeBFTRootScaleOperator(operator, prefix, writer); + break; + case UNIFORM_SUBTREE_PRUNE_REGRAFT: + writeUniformSPROperator(operator, prefix, writer); + break; default: throw new IllegalArgumentException("Unknown operator type"); } @@ -736,7 +740,7 @@ private void writeBFTUniformNodeHeightOperator(Operator operator, String treeMod writer.writeCloseTag(NodeHeightOperatorParser.NODE_HEIGHT_OPERATOR); } - private void writeBFTUniformRootScaleOperator(Operator operator, String treeModelPrefix, XMLWriter writer) { + private void writeBFTRootScaleOperator(Operator operator, String treeModelPrefix, XMLWriter writer) { writer.writeOpenTag(NodeHeightOperatorParser.NODE_HEIGHT_OPERATOR, // should this be in the class and not the parser? new Attribute[]{ new Attribute.Default("type",NodeHeightOperatorParser.OperatorType.SCALEROOT.toString()), @@ -749,6 +753,15 @@ private void writeBFTUniformRootScaleOperator(Operator operator, String treeMode writer.writeCloseTag(NodeHeightOperatorParser.NODE_HEIGHT_OPERATOR); } + private void writeUniformSPROperator(Operator operator, String treeModelPrefix, XMLWriter writer) { + writer.writeOpenTag(UniformSubtreePruneRegraftParser.UNIFORM_SUBTREE_PRUNE_REGRAFT, // should this be in the class and not the parser? + new Attribute[]{ + getWeightAttribute(operator.getWeight()) + }); + writer.writeIDref(ConstrainedTreeModel.CONSTRAINED_TREE_MODEL, treeModelPrefix + DefaultTreeModel.TREE_MODEL); + writer.writeCloseTag(UniformSubtreePruneRegraftParser.UNIFORM_SUBTREE_PRUNE_REGRAFT); + } + // tuneable version of FHSPR but not currently being used private void writeSubtreeJumpOperator(Operator operator, String treeModelPrefix, XMLWriter writer) { diff --git a/src/dr/app/beauti/options/PartitionTreeModel.java b/src/dr/app/beauti/options/PartitionTreeModel.java index 4517cac9b0..7a92877891 100644 --- a/src/dr/app/beauti/options/PartitionTreeModel.java +++ b/src/dr/app/beauti/options/PartitionTreeModel.java @@ -147,21 +147,27 @@ public void initModelParametersAndOpererators() { // does STL works on constrained trees? createOperator("subtreeLeap", "Tree", "Performs the subtree-leap rearrangement of the tree", "tree", - OperatorType.SUBTREE_LEAP, 1.0, weight); + OperatorType.SUBTREE_LEAP, 1.0, weight); + createOperator("uniformSPG", "Tree", "Performs the subtree prune regraft within a polytomony rearrangement of the tree", "tree", + OperatorType.UNIFORM_SUBTREE_PRUNE_REGRAFT, -1, weight); + createOperator("nodeHeight-uniform","Tree", "Draws new internal node heights on constrained tree uniformally","tree", - OperatorType.NODE_HEIGHT_OPERATOR_UNIFORM,-1.0, treeWeights); + OperatorType.NODE_HEIGHT_OPERATOR_UNIFORM,-1.0, weight); // In the TB setting this will almost always give the same likelihood since coalescent doesn't change // and if we are in the non mutation zone the treelikelihood will be the same. - createOperator("FHSPR", "Tree", "Performs the fixed-height subtree prune/regraft of the tree", "tree", - OperatorType.FIXED_HEIGHT_SUBTREE_PRUNE_REGRAFT, 1.0, weight); + // not compatible with constrained tree right now. + // createOperator("FHSPR", "Tree", "Performs the fixed-height subtree prune/regraft of the tree", "tree", + // OperatorType.FIXED_HEIGHT_SUBTREE_PRUNE_REGRAFT, 1.0, weight); createOperator("narrowExchange", "Tree", "Performs local rearrangements of the tree", "tree", OperatorType.NARROW_EXCHANGE, -1, weight); + + weight = Math.max(weight / 100, 3); + createOperator("wideExchange", "Tree", "Performs global rearrangements of the tree", "tree", OperatorType.WIDE_EXCHANGE, -1, weight); - weight = Math.max(weight / 10, 3); // these work on bft tree models createOperator("nodeHeight-root","Tree", "Draws new root height on constrained tree","tree", @@ -210,14 +216,18 @@ public List selectOperators(List operators) { if (isUsingEmpiricalTrees()) { operators.add(getOperator("empiricalTreeSwap")); } else if(isUsingThorneyBEAST()){ + + operators.add(getOperator("nodeHeight-uniform")); + operators.add(getOperator("nodeHeight-root")); + // TODO check if there are polytomies otherwise these will error out + operators.add(getOperator("uniformSPG")); operators.add(getOperator("narrowExchange")); operators.add(getOperator("wideExchange")); operators.add(getOperator("wilsonBalding")); + //TODO add back in once operators is functional + // operators.add(getOperator("FHSPR")); - operators.add(getOperator("FHSPR")); - operators.add(getOperator("nodeHeight-uniform")); - operators.add(getOperator("nodeHeight-root")); }else { diff --git a/src/dr/app/beauti/types/OperatorType.java b/src/dr/app/beauti/types/OperatorType.java index 0b68c75ba1..daa6a518c3 100644 --- a/src/dr/app/beauti/types/OperatorType.java +++ b/src/dr/app/beauti/types/OperatorType.java @@ -62,6 +62,7 @@ public enum OperatorType { SUBTREE_SLIDE("subtreeSlide"), FIXED_HEIGHT_SUBTREE_PRUNE_REGRAFT("fixedHeightSPR"), SUBTREE_LEAP("subtreeLeap"), + UNIFORM_SUBTREE_PRUNE_REGRAFT("uniformSPG"), ADAPTIVE_MULTIVARIATE("adaptiveMultivariate"), NARROW_EXCHANGE("narrowExchange"), WIDE_EXCHANGE("wideExchange"), diff --git a/src/dr/evomodelxml/operators/NodeHeightOperatorParser.java b/src/dr/evomodelxml/operators/NodeHeightOperatorParser.java index 0618ef2072..6928a8b819 100644 --- a/src/dr/evomodelxml/operators/NodeHeightOperatorParser.java +++ b/src/dr/evomodelxml/operators/NodeHeightOperatorParser.java @@ -46,8 +46,8 @@ public class NodeHeightOperatorParser extends AbstractXMLObjectParser { public enum OperatorType { UNIFORM("uniform"), RANDOMWALK("random walk"), - SCALEROOT("scale root"), - SCALEALL("scale all internal"); + SCALEROOT("scaleRoot"), + SCALEALL("scaleAll"); // MULTIMOVEUNIFORM("multiMoveUniform"); // -JT the order in which nodes are picked matters but there is more than // one way to pick the nodes I don't trust the multimove operator From 3661e1020aa52b1ed356017d14e86e8b0de3f614 Mon Sep 17 00:00:00 2001 From: jtmccr1 Date: Fri, 12 Jul 2024 12:26:48 -0500 Subject: [PATCH 10/28] thorney beast uses bft-intervals nows --- .../beauti/generator/TreePriorGenerator.java | 77 ++++++++++++++++--- 1 file changed, 65 insertions(+), 12 deletions(-) diff --git a/src/dr/app/beauti/generator/TreePriorGenerator.java b/src/dr/app/beauti/generator/TreePriorGenerator.java index c39b0b4dd2..13f9892566 100644 --- a/src/dr/app/beauti/generator/TreePriorGenerator.java +++ b/src/dr/app/beauti/generator/TreePriorGenerator.java @@ -36,10 +36,13 @@ import dr.app.beauti.util.XMLWriter; import dr.evolution.util.Taxa; import dr.evolution.util.Units; +import dr.evomodel.bigfasttree.BigFastTreeIntervals; +import dr.evomodel.bigfasttree.thorney.ConstrainedTreeModel; import dr.evomodel.coalescent.GMRFSkyrideGradient; import dr.evomodel.tree.DefaultTreeModel; import dr.evomodel.tree.TreeModel; import dr.evomodelxml.CSVExporterParser; +import dr.evomodelxml.bigfasttree.BigFastTreeIntervalsParser; import dr.evomodelxml.coalescent.*; import dr.evomodelxml.coalescent.demographicmodel.ConstantPopulationModelParser; import dr.evomodelxml.coalescent.demographicmodel.ExpansionModelParser; @@ -577,9 +580,19 @@ void writePriorLikelihood(PartitionTreeModel model, XMLWriter writer) { writeParameter(prior.getParameter("skyride.precision"), 1, writer); writer.writeCloseTag(GMRFSkyrideLikelihoodParser.PRECISION_PARAMETER); - writer.writeOpenTag(GMRFSkyrideLikelihoodParser.POPULATION_TREE); - writer.writeIDref(DefaultTreeModel.TREE_MODEL, prefix + DefaultTreeModel.TREE_MODEL); - writer.writeCloseTag(GMRFSkyrideLikelihoodParser.POPULATION_TREE); + + if(model.isUsingThorneyBEAST()){ + writer.writeOpenTag(GMRFSkyrideLikelihoodParser.INTERVALS); + writer.writeOpenTag(BigFastTreeIntervalsParser.TREE_INTERVALS); + writer.writeIDref(ConstrainedTreeModel.CONSTRAINED_TREE_MODEL, prefix + DefaultTreeModel.TREE_MODEL); + writer.writeCloseTag(BigFastTreeIntervalsParser.TREE_INTERVALS); + writer.writeCloseTag(GMRFSkyrideLikelihoodParser.INTERVALS); + }else{ + writer.writeOpenTag(GMRFSkyrideLikelihoodParser.POPULATION_TREE); + writer.writeIDref(DefaultTreeModel.TREE_MODEL, prefix + DefaultTreeModel.TREE_MODEL); + writer.writeCloseTag(GMRFSkyrideLikelihoodParser.POPULATION_TREE); + } + writer.writeCloseTag(GMRFSkyrideLikelihoodParser.SKYLINE_LIKELIHOOD); @@ -599,9 +612,17 @@ void writePriorLikelihood(PartitionTreeModel model, XMLWriter writer) { writer.writeOpenTag(CoalescentLikelihoodParser.MODEL); writeNodeHeightPriorModelRef(prior, writer); writer.writeCloseTag(CoalescentLikelihoodParser.MODEL); - writer.writeOpenTag(CoalescentLikelihoodParser.POPULATION_TREE); - writer.writeIDref(DefaultTreeModel.TREE_MODEL, prefix + DefaultTreeModel.TREE_MODEL); - writer.writeCloseTag(CoalescentLikelihoodParser.POPULATION_TREE); + if(model.isUsingThorneyBEAST()){ + writer.writeOpenTag(GMRFSkyrideLikelihoodParser.INTERVALS); + writer.writeOpenTag(BigFastTreeIntervalsParser.TREE_INTERVALS); + writer.writeIDref(ConstrainedTreeModel.CONSTRAINED_TREE_MODEL, prefix + DefaultTreeModel.TREE_MODEL); + writer.writeCloseTag(BigFastTreeIntervalsParser.TREE_INTERVALS); + writer.writeCloseTag(GMRFSkyrideLikelihoodParser.INTERVALS); + }else{ + writer.writeOpenTag(CoalescentLikelihoodParser.POPULATION_TREE); + writer.writeIDref(DefaultTreeModel.TREE_MODEL, prefix + DefaultTreeModel.TREE_MODEL); + writer.writeCloseTag(CoalescentLikelihoodParser.POPULATION_TREE); + } writer.writeCloseTag(CoalescentLikelihoodParser.COALESCENT_LIKELIHOOD); } } @@ -692,17 +713,49 @@ void writeMultiLociTreePriors(PartitionTreePrior prior, XMLWriter writer) { cutOff.setInitial(skyGridInterval); writeParameter(cutOff, 1, writer); writer.writeCloseTag(GMRFSkyrideLikelihoodParser.CUT_OFF); - - writer.writeOpenTag(GMRFSkyrideLikelihoodParser.POPULATION_TREE); + // TODO Add all linked trees if (options.isShareSameTreePrior()) { - for (PartitionTreeModel thisModel : options.getPartitionTreeModels()) { - writer.writeIDref(DefaultTreeModel.TREE_MODEL, thisModel.getPrefix() + DefaultTreeModel.TREE_MODEL); + Boolean usingTB=true; + for(PartitionTreeModel treeModel: options.getPartitionTreeModels()){ + if(!treeModel.isUsingThorneyBEAST()){ + usingTB=false; + break; + } + } + if(usingTB){ + writer.writeOpenTag(GMRFSkyrideLikelihoodParser.INTERVALS); + for (PartitionTreeModel thisModel : options.getPartitionTreeModels()) { + writer.writeOpenTag(BigFastTreeIntervalsParser.TREE_INTERVALS); + writer.writeIDref(ConstrainedTreeModel.CONSTRAINED_TREE_MODEL, thisModel.getPrefix() + DefaultTreeModel.TREE_MODEL); + writer.writeCloseTag(BigFastTreeIntervalsParser.TREE_INTERVALS); + } + writer.writeCloseTag(GMRFSkyrideLikelihoodParser.INTERVALS); + }else{ + writer.writeOpenTag(GMRFSkyrideLikelihoodParser.POPULATION_TREE); + for (PartitionTreeModel thisModel : options.getPartitionTreeModels()) { + writer.writeIDref(DefaultTreeModel.TREE_MODEL, thisModel.getPrefix() + DefaultTreeModel.TREE_MODEL); + } + writer.writeCloseTag(GMRFSkyrideLikelihoodParser.POPULATION_TREE); } } else { - writer.writeIDref(DefaultTreeModel.TREE_MODEL, options.getPartitionTreeModels(prior).get(0).getPrefix() + DefaultTreeModel.TREE_MODEL); + + Boolean usingTB= options.getPartitionTreeModels(prior).get(0).isUsingThorneyBEAST(); + if(usingTB){ + writer.writeOpenTag(GMRFSkyrideLikelihoodParser.INTERVALS); + writer.writeOpenTag(BigFastTreeIntervalsParser.TREE_INTERVALS); + writer.writeIDref(ConstrainedTreeModel.CONSTRAINED_TREE_MODEL, options.getPartitionTreeModels(prior).get(0).getPrefix() + DefaultTreeModel.TREE_MODEL); + writer.writeCloseTag(BigFastTreeIntervalsParser.TREE_INTERVALS); + writer.writeCloseTag(GMRFSkyrideLikelihoodParser.INTERVALS); + + }else{ + writer.writeOpenTag(GMRFSkyrideLikelihoodParser.POPULATION_TREE); + writer.writeIDref(DefaultTreeModel.TREE_MODEL, options.getPartitionTreeModels(prior).get(0).getPrefix() + DefaultTreeModel.TREE_MODEL); + writer.writeCloseTag(GMRFSkyrideLikelihoodParser.POPULATION_TREE); + } } - writer.writeCloseTag(GMRFSkyrideLikelihoodParser.POPULATION_TREE); + + writer.writeCloseTag(GMRFSkyrideLikelihoodParser.SKYGRID_LIKELIHOOD); From 77fb51d1ff95f044382d3c839ebc53ee8add4267 Mon Sep 17 00:00:00 2001 From: jtmccr1 Date: Fri, 12 Jul 2024 14:35:51 -0500 Subject: [PATCH 11/28] removes unneeded components --- .../beauti/components/thorney/ThorneyComponentFactory.java | 5 ----- .../beauti/components/thorney/ThorneyComponentGenerator.java | 5 ----- .../beauti/components/thorney/ThorneyComponentOptions.java | 5 ----- .../app/beauti/components/thorney/ThorneySubstModelType.java | 5 ----- 4 files changed, 20 deletions(-) delete mode 100644 src/dr/app/beauti/components/thorney/ThorneyComponentFactory.java delete mode 100644 src/dr/app/beauti/components/thorney/ThorneyComponentGenerator.java delete mode 100644 src/dr/app/beauti/components/thorney/ThorneyComponentOptions.java delete mode 100644 src/dr/app/beauti/components/thorney/ThorneySubstModelType.java diff --git a/src/dr/app/beauti/components/thorney/ThorneyComponentFactory.java b/src/dr/app/beauti/components/thorney/ThorneyComponentFactory.java deleted file mode 100644 index c4db0d7a3a..0000000000 --- a/src/dr/app/beauti/components/thorney/ThorneyComponentFactory.java +++ /dev/null @@ -1,5 +0,0 @@ -package dr.app.beauti.components.thorney; - -public class ThorneyComponentFactory { - -} diff --git a/src/dr/app/beauti/components/thorney/ThorneyComponentGenerator.java b/src/dr/app/beauti/components/thorney/ThorneyComponentGenerator.java deleted file mode 100644 index a017c976d2..0000000000 --- a/src/dr/app/beauti/components/thorney/ThorneyComponentGenerator.java +++ /dev/null @@ -1,5 +0,0 @@ -package dr.app.beauti.components.thorney; - -public class ThorneyComponentGenerator { - -} diff --git a/src/dr/app/beauti/components/thorney/ThorneyComponentOptions.java b/src/dr/app/beauti/components/thorney/ThorneyComponentOptions.java deleted file mode 100644 index 9d35b4ed43..0000000000 --- a/src/dr/app/beauti/components/thorney/ThorneyComponentOptions.java +++ /dev/null @@ -1,5 +0,0 @@ -package dr.app.beauti.components.thorney; - -public class ThorneyComponentOptions { - -} diff --git a/src/dr/app/beauti/components/thorney/ThorneySubstModelType.java b/src/dr/app/beauti/components/thorney/ThorneySubstModelType.java deleted file mode 100644 index 88c79d04ca..0000000000 --- a/src/dr/app/beauti/components/thorney/ThorneySubstModelType.java +++ /dev/null @@ -1,5 +0,0 @@ -package dr.app.beauti.components.thorney; - -public class ThorneySubstModelType { - -} From 0fe7bfbf44e1b95d3088c9aa56c4e81c542e29e9 Mon Sep 17 00:00:00 2001 From: jtmccr1 Date: Fri, 12 Jul 2024 14:36:46 -0500 Subject: [PATCH 12/28] trying out clock models with tb --- src/dr/app/beauti/options/PartitionClockModel.java | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/dr/app/beauti/options/PartitionClockModel.java b/src/dr/app/beauti/options/PartitionClockModel.java index c236a2e8f3..9cd7c4af7b 100644 --- a/src/dr/app/beauti/options/PartitionClockModel.java +++ b/src/dr/app/beauti/options/PartitionClockModel.java @@ -550,8 +550,9 @@ public List selectOperators(List operators) { List ops = new ArrayList(); if (options.hasData()) { - if (getDataType().getType() != DataType.TREE) { + // if (getDataType().getType() != DataType.TREE) { Operator rateOperator = getOperator("clock.rate"); + switch (clockType) { case STRICT_CLOCK: ops.add(rateOperator); @@ -667,7 +668,7 @@ public List selectOperators(List operators) { throw new IllegalArgumentException("Unknown clock model"); } - } + // } } Parameter allMuNus = getParameter(options.useNuRelativeRates() ? "allNus" : "allMus"); From 7de04b32e5e28dc0347ea546fc8f888c5353ea05 Mon Sep 17 00:00:00 2001 From: jtmccr1 Date: Fri, 12 Jul 2024 14:55:33 -0500 Subject: [PATCH 13/28] proxy parameters so we can use usual node height operators --- .../app/beast/development_parsers.properties | 4 +- .../thorney/RootHeightProxyParameter.java | 120 ++++++++++++++++++ .../discrete/NodeHeightProxyParameter.java | 40 +++++- 3 files changed, 162 insertions(+), 2 deletions(-) create mode 100644 src/dr/evomodel/bigfasttree/thorney/RootHeightProxyParameter.java diff --git a/src/dr/app/beast/development_parsers.properties b/src/dr/app/beast/development_parsers.properties index f741317644..37a13dcc62 100644 --- a/src/dr/app/beast/development_parsers.properties +++ b/src/dr/app/beast/development_parsers.properties @@ -1,7 +1,7 @@ # # development_parsers.properties # -# Copyright © 2002-2024 the BEAST Development Team +# Copyright � 2002-2024 the BEAST Development Team # http://beast.community/about # # This file is part of BEAST. @@ -264,6 +264,8 @@ dr.evomodelxml.bigfasttree.thorney.ThorneyTreeGradientParser dr.evomodelxml.bigfasttree.thorney.UniformSubtreePruneRegraftParser dr.evomodel.bigfasttree.thorney.ZeroMutationMasker dr.evomodelxml.bigfasttree.thorney.SubtreeRootHeightStatisticParser +dr.evomodel.bigfasttree.thorney.RootHeightProxyParameter + # GLM dr.inferencexml.operators.MaskMoveOperatorParser dr.evomodelxml.continuous.hmc.GlmSubstitutionModelGradientParser diff --git a/src/dr/evomodel/bigfasttree/thorney/RootHeightProxyParameter.java b/src/dr/evomodel/bigfasttree/thorney/RootHeightProxyParameter.java new file mode 100644 index 0000000000..29eed5a0d7 --- /dev/null +++ b/src/dr/evomodel/bigfasttree/thorney/RootHeightProxyParameter.java @@ -0,0 +1,120 @@ +package dr.evomodel.bigfasttree.thorney; + +import dr.evolution.tree.NodeRef; +import dr.evomodel.tree.TreeChangedEvent; +import dr.evomodel.tree.TreeModel; +import dr.inference.model.Bounds; +import dr.inference.model.Parameter; +import dr.xml.*; + + +// see NodeHeightProxyParameter.java + +public class RootHeightProxyParameter extends Parameter.Proxy implements Bounds { + private TreeModel tree; + public RootHeightProxyParameter(String name, + TreeModel tree) { + super(name, 1); + this.tree = tree; + } + + public TreeModel getTree() { + return tree; + } + + + + @Override + public double getParameterValue(int dim) { + return tree.getNodeHeight(tree.getRoot()); + } + + @Override + public void setParameterValue(int dim, double value) { + tree.setNodeHeight(tree.getRoot(), value); + tree.pushTreeChangedEvent(tree.getRoot()); + } + + @Override + public void setParameterValueQuietly(int dim, double value) { + tree.setNodeHeightQuietly(tree.getRoot(), value); + } + @Override + public Bounds getBounds() { + return this; + } + //bounds implementation + @Override + public Double getUpperLimit(int dimension) { + return Double.POSITIVE_INFINITY; + } + + @Override + public Double getLowerLimit(int dimension) { + // TODO Auto-generated method stub + NodeRef node = tree.getRoot(); + double max = 0.0; + for(int i = 0; i < tree.getChildCount(node); i++) { + max = Math.max(max, tree.getNodeHeight(tree.getChild(node,i))); + } + return max; + } + + @Override + public int getBoundsDimension() { + return this.getDimension(); + } + public String toString() { + StringBuilder buffer = new StringBuilder(String.valueOf(getParameterValue(0))); + Bounds bounds = null; + + for (int i = 1; i < getDimension(); i++) { + buffer.append("\t").append(String.valueOf(getParameterValue(i))); + } + return buffer.toString(); + } + + @Override + public void fireParameterChangedEvent() { + tree.pushTreeChangedEvent(TreeChangedEvent.create(true, true)); + } + + @Override + public void setParameterValueNotifyChangedAll(int dim, double value) { + setParameterValue(dim, value); + } + + private static final String ROOT_HEIGHT_PARAMETER = "RootHeightProxyParameter"; + + public static AbstractXMLObjectParser PARSER = new AbstractXMLObjectParser() { + @Override + public Object parseXMLObject(XMLObject xo) throws XMLParseException { + TreeModel tree = (TreeModel) xo.getChild(TreeModel.class); + return new RootHeightProxyParameter(ROOT_HEIGHT_PARAMETER, tree); + } + + @Override + public XMLSyntaxRule[] getSyntaxRules() { + return new XMLSyntaxRule[]{ + new ElementRule(TreeModel.class), + }; + } + + @Override + public String getParserDescription() { + return null; + } + + @Override + public Class getReturnType() { + return RootHeightProxyParameter.class; + } + + @Override + public String getParserName() { + return ROOT_HEIGHT_PARAMETER; + } + }; +} + + diff --git a/src/dr/evomodel/treedatalikelihood/discrete/NodeHeightProxyParameter.java b/src/dr/evomodel/treedatalikelihood/discrete/NodeHeightProxyParameter.java index 83a509fb3a..0218af3c96 100644 --- a/src/dr/evomodel/treedatalikelihood/discrete/NodeHeightProxyParameter.java +++ b/src/dr/evomodel/treedatalikelihood/discrete/NodeHeightProxyParameter.java @@ -27,6 +27,7 @@ package dr.evomodel.treedatalikelihood.discrete; +import dr.evolution.tree.NodeRef; import dr.evomodel.tree.TreeChangedEvent; import dr.evomodel.tree.TreeModel; import dr.evomodel.tree.TreeParameterModel; @@ -38,7 +39,7 @@ * @author Marc A. Suchard * @author Xiang Ji */ -public class NodeHeightProxyParameter extends Parameter.Proxy { +public class NodeHeightProxyParameter extends Parameter.Proxy implements Bounds { private TreeModel tree; private TreeParameterModel indexHelper; @@ -51,6 +52,7 @@ public NodeHeightProxyParameter(String name, this.indexHelper = new TreeParameterModel(tree, new Parameter.Default(includeRoot ? tree.getInternalNodeCount() : tree.getInternalNodeCount() - 1, 0.0), includeRoot); + } public TreeModel getTree() { @@ -76,7 +78,41 @@ public void setParameterValue(int dim, double value) { public void setParameterValueQuietly(int dim, double value) { tree.setNodeHeightQuietly(tree.getNode(getNodeNumber(dim)), value); } + @Override + public Bounds getBounds() { + return this; + } + //bounds implementation + @Override + public Double getUpperLimit(int dimension) { + NodeRef node = tree.getNode(getNodeNumber(dimension)); + if(tree.isRoot(node)){ + return Double.POSITIVE_INFINITY; + }else{ + return tree.getNodeHeight(tree.getParent(node)); + } + + } + @Override + public Double getLowerLimit(int dimension) { + // TODO Auto-generated method stub + NodeRef node = tree.getNode(getNodeNumber(dimension)); + if (tree.isExternal(node)) { + return 0.0; + } else { + double max = 0.0; + for(int i = 0; i < tree.getChildCount(node); i++) { + max = Math.max(max, tree.getNodeHeight(tree.getChild(node,i))); + } + return max; + } + } + + @Override + public int getBoundsDimension() { + return this.getDimension(); + } public String toString() { StringBuilder buffer = new StringBuilder(String.valueOf(getParameterValue(0))); Bounds bounds = null; @@ -132,3 +168,5 @@ public String getParserName() { } }; } + + From b11d856d222782b0928fbd1d069c136bacb05e14 Mon Sep 17 00:00:00 2001 From: jtmccr1 Date: Fri, 12 Jul 2024 15:30:17 -0500 Subject: [PATCH 14/28] adds node height proxies and standard operators --- .../beauti/generator/TreeModelGenerator.java | 28 +++++++++++++++++ .../beauti/options/PartitionTreeModel.java | 30 ++++++++++--------- .../discrete/NodeHeightProxyParameter.java | 2 +- 3 files changed, 45 insertions(+), 15 deletions(-) diff --git a/src/dr/app/beauti/generator/TreeModelGenerator.java b/src/dr/app/beauti/generator/TreeModelGenerator.java index 8ac197f708..3d1a4eaa10 100644 --- a/src/dr/app/beauti/generator/TreeModelGenerator.java +++ b/src/dr/app/beauti/generator/TreeModelGenerator.java @@ -32,8 +32,10 @@ import dr.app.beauti.options.PartitionTreeModel; import dr.app.beauti.util.XMLWriter; import dr.evomodel.bigfasttree.thorney.ConstrainedTreeModel; +import dr.evomodel.bigfasttree.thorney.RootHeightProxyParameter; import dr.evomodel.tree.DefaultTreeModel; import dr.evomodel.tree.EmpiricalTreeDistributionModel; +import dr.evomodel.treedatalikelihood.discrete.NodeHeightProxyParameter; import dr.evomodelxml.bigfasttree.thorney.ConstrainedTreeModelParser; import dr.evomodelxml.coalescent.OldCoalescentSimulatorParser; import dr.evomodelxml.tree.*; @@ -101,6 +103,32 @@ void writeConstrainedTreeModel(PartitionTreeModel model, XMLWriter writer) { writer.writeCloseTag(ConstrainedTreeModel.CONSTRAINED_TREE_MODEL); + writer.writeComment("Parameter proxies for node heights"); + + + writer.writeOpenTag(RootHeightProxyParameter.PARSER.getParserName(),new Attribute.Default(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(XMLParser.ID, treeModelName + "." + "internalNodeHeights"), + new Attribute.Default(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(XMLParser.ID, treeModelName + "." + "allInternalNodeHeights"), + new Attribute.Default(NodeHeightProxyParameter.INCLUDE_ROOT, "true") + }); + writer.writeIDref(ConstrainedTreeModelParser.CONSTRAINTS_TREE, treeModelName); + + writer.writeCloseTag(NodeHeightProxyParameter.PARSER.getParserName()); + writeTreeModelStatistics(model, writer); diff --git a/src/dr/app/beauti/options/PartitionTreeModel.java b/src/dr/app/beauti/options/PartitionTreeModel.java index 7a92877891..190e210fa6 100644 --- a/src/dr/app/beauti/options/PartitionTreeModel.java +++ b/src/dr/app/beauti/options/PartitionTreeModel.java @@ -142,7 +142,8 @@ public void initModelParametersAndOpererators() { createOperator("FHSPR", "Tree", "Performs the fixed-height subtree prune/regraft of the tree", "tree", OperatorType.FIXED_HEIGHT_SUBTREE_PRUNE_REGRAFT, 1.0, weight); } else { - //Thorney BEAST operators here? + //Thorney BEAST operators + // Big weights operators double weight = Math.max(options.taxonList.getTaxonCount(), 30); // does STL works on constrained trees? @@ -152,26 +153,30 @@ public void initModelParametersAndOpererators() { OperatorType.UNIFORM_SUBTREE_PRUNE_REGRAFT, -1, weight); - createOperator("nodeHeight-uniform","Tree", "Draws new internal node heights on constrained tree uniformally","tree", - OperatorType.NODE_HEIGHT_OPERATOR_UNIFORM,-1.0, weight); - + createOperator("treeBitMove", "Tree", "Swaps the rates and change locations of local clocks", "tree", + OperatorType.TREE_BIT_MOVE, -1.0, treeWeights); + + createOperator("uniformHeights", "Internal node heights", "Draws new internal node heights uniformally", + "treeModel.internalNodeHeights", OperatorType.UNIFORM, -1, weight); + + // This scale operator is used instead of the up/down if the rate is fixed. + new Operator.Builder("treeModel.allInternalNodeHeights", "Scales all internal node heights in tree", getParameter("treeModel.allInternalNodeHeights"), OperatorType.SCALE_ALL, 0.75, rateWeights).build(operators); + // In the TB setting this will almost always give the same likelihood since coalescent doesn't change // and if we are in the non mutation zone the treelikelihood will be the same. // not compatible with constrained tree right now. // createOperator("FHSPR", "Tree", "Performs the fixed-height subtree prune/regraft of the tree", "tree", // OperatorType.FIXED_HEIGHT_SUBTREE_PRUNE_REGRAFT, 1.0, weight); + createOperator("narrowExchange", "Tree", "Performs local rearrangements of the tree", "tree", OperatorType.NARROW_EXCHANGE, -1, weight); weight = Math.max(weight / 100, 3); + createScaleOperator("treeModel.rootHeight", demoTuning, weight); createOperator("wideExchange", "Tree", "Performs global rearrangements of the tree", "tree", OperatorType.WIDE_EXCHANGE, -1, weight); - - // these work on bft tree models - createOperator("nodeHeight-root","Tree", "Draws new root height on constrained tree","tree", - OperatorType.NODE_HEIGHT_OPERATOR_ROOT,demoTuning, weight); createOperator("wilsonBalding", "Tree", "Performs the Wilson-Balding rearrangement of the tree", "tree", OperatorType.WILSON_BALDING, -1, weight); @@ -189,7 +194,7 @@ public List selectParameters(List parameters) { // get parameter so their id prefix can be set. getParameter("tree"); - if(isUsingEmpiricalTrees()||isUsingThorneyBEAST()){ + if(isUsingEmpiricalTrees()){ return parameters; } getParameter("treeModel.internalNodeHeights"); @@ -217,8 +222,8 @@ public List selectOperators(List operators) { operators.add(getOperator("empiricalTreeSwap")); } else if(isUsingThorneyBEAST()){ - operators.add(getOperator("nodeHeight-uniform")); - operators.add(getOperator("nodeHeight-root")); + operators.add(getOperator("treeModel.rootHeight")); + operators.add(getOperator("uniformHeights")); // TODO check if there are polytomies otherwise these will error out operators.add(getOperator("uniformSPG")); operators.add(getOperator("narrowExchange")); @@ -227,9 +232,6 @@ public List selectOperators(List operators) { //TODO add back in once operators is functional // operators.add(getOperator("FHSPR")); - - - }else { if (treePartitionData == null) { Operator subtreeSlideOp = getOperator("subtreeSlide"); diff --git a/src/dr/evomodel/treedatalikelihood/discrete/NodeHeightProxyParameter.java b/src/dr/evomodel/treedatalikelihood/discrete/NodeHeightProxyParameter.java index 0218af3c96..53312c6d2d 100644 --- a/src/dr/evomodel/treedatalikelihood/discrete/NodeHeightProxyParameter.java +++ b/src/dr/evomodel/treedatalikelihood/discrete/NodeHeightProxyParameter.java @@ -134,7 +134,7 @@ public void setParameterValueNotifyChangedAll(int dim, double value) { } private static final String NODE_HEIGHT_PARAMETER = "nodeHeightProxyParameter"; - private static final String INCLUDE_ROOT = "rootNode"; + public static final String INCLUDE_ROOT = "rootNode"; public static AbstractXMLObjectParser PARSER = new AbstractXMLObjectParser() { @Override From 062fc436caa5a35cc2de8a8a89d22b0c9609584e Mon Sep 17 00:00:00 2001 From: jtmccr1 Date: Fri, 12 Jul 2024 15:44:39 -0500 Subject: [PATCH 15/28] fixes bug in rate covariance that failed if parent was null --- src/dr/evomodel/tree/RateCovarianceStatistic.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/dr/evomodel/tree/RateCovarianceStatistic.java b/src/dr/evomodel/tree/RateCovarianceStatistic.java index 743ca891d8..9d7b3b3159 100644 --- a/src/dr/evomodel/tree/RateCovarianceStatistic.java +++ b/src/dr/evomodel/tree/RateCovarianceStatistic.java @@ -72,7 +72,7 @@ public double getStatisticValue(int dim) { for (int i = 0; i < n; i++) { NodeRef child = tree.getNode(i); NodeRef parent = tree.getParent(child); - if (parent != null & !tree.isRoot(parent)) { + if (parent != null && !tree.isRoot(parent)) { childRate[index] = branchRateModel.getBranchRate(tree, child); parentRate[index] = branchRateModel.getBranchRate(tree, parent); index += 1; From 8128df3a2b074e858a1cb080d10ea1fe503eb44e Mon Sep 17 00:00:00 2001 From: jtmccr1 Date: Sat, 27 Jul 2024 10:52:38 -0500 Subject: [PATCH 16/28] adds beauti generated example for 1K SARS2 --- examples/1K.thorney.HMC.xml | 3395 ---------------------------- examples/1K_SARS-CoV-2-thorney.xml | 3257 ++++++++++++++++++++++++++ examples/Data/1K_SARS-CoV-2.nexus | 8 + 3 files changed, 3265 insertions(+), 3395 deletions(-) delete mode 100644 examples/1K.thorney.HMC.xml create mode 100644 examples/1K_SARS-CoV-2-thorney.xml create mode 100644 examples/Data/1K_SARS-CoV-2.nexus diff --git a/examples/1K.thorney.HMC.xml b/examples/1K.thorney.HMC.xml deleted file mode 100644 index 1d53ad70e9..0000000000 --- a/examples/1K.thorney.HMC.xml +++ /dev/null @@ -1,3395 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/examples/Data/1K_SARS-CoV-2.nexus b/examples/Data/1K_SARS-CoV-2.nexus new file mode 100644 index 0000000000..478500a793 --- /dev/null +++ b/examples/Data/1K_SARS-CoV-2.nexus @@ -0,0 +1,8 @@ +#NEXUS +BEGIN TAXA; + DIMENSIONS NTAX=1000; + TAXLABELS 'Wuhan/WH04/2020|2020-01-05' 'Australia/NSW01/2020|2020-01-24' 'Jiujiang/JX22/2020|2020-01-22' 'Wuhan/HBCDC-HB-03/2020|2020-01-18' 'Yunnan/IVDC-YN-003/2020|2020-01-17' 'Guangzhou/GZMU0099/2020|2020-02-20' 'Wuhan/HBCDC-HB-02/2020|2020-01-17' 'Nanchang/JX14/2020|2020-01-21' 'Belgium/GHB-03021/2020|2020-02-03' 'Australia/VIC13/2020|2020-01-31' 'Singapore/383/2020|2020-02-15' 'Guangdong/MZ01/2020|2020-02-13' 'Shandong/LY006-2/2020|2020-01-25' 'England/PHEC-22387/2020|2020-06-03' 'Korea/KCDC2002/2020|2020-01-30' 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+END; From ad4147c8ecfc60a83f847d932715f77c0e07c898 Mon Sep 17 00:00:00 2001 From: jtmccr1 Date: Wed, 7 Aug 2024 15:45:33 -0300 Subject: [PATCH 17/28] removing comments --- src/dr/app/beauti/sitemodelspanel/PartitionModelPanel.java | 3 +-- src/dr/evomodelxml/operators/NodeHeightOperatorParser.java | 4 ++-- 2 files changed, 3 insertions(+), 4 deletions(-) diff --git a/src/dr/app/beauti/sitemodelspanel/PartitionModelPanel.java b/src/dr/app/beauti/sitemodelspanel/PartitionModelPanel.java index 058593b3b8..3381c8fb9a 100644 --- a/src/dr/app/beauti/sitemodelspanel/PartitionModelPanel.java +++ b/src/dr/app/beauti/sitemodelspanel/PartitionModelPanel.java @@ -727,8 +727,7 @@ private void setupPanel() { break; case DataType.TREE: - //DO all sorts of things I haven't figured out yet - // System.out.println("Tree data type in PartitionModelPanel setupPanel"); + // Do nothing break; default: throw new IllegalArgumentException("Unknown data type"); diff --git a/src/dr/evomodelxml/operators/NodeHeightOperatorParser.java b/src/dr/evomodelxml/operators/NodeHeightOperatorParser.java index 6928a8b819..0618ef2072 100644 --- a/src/dr/evomodelxml/operators/NodeHeightOperatorParser.java +++ b/src/dr/evomodelxml/operators/NodeHeightOperatorParser.java @@ -46,8 +46,8 @@ public class NodeHeightOperatorParser extends AbstractXMLObjectParser { public enum OperatorType { UNIFORM("uniform"), RANDOMWALK("random walk"), - SCALEROOT("scaleRoot"), - SCALEALL("scaleAll"); + SCALEROOT("scale root"), + SCALEALL("scale all internal"); // MULTIMOVEUNIFORM("multiMoveUniform"); // -JT the order in which nodes are picked matters but there is more than // one way to pick the nodes I don't trust the multimove operator From 344a22e58fac1f9fb9e0bc8ae5983ff2af9ebc5d Mon Sep 17 00:00:00 2001 From: jtmccr1 Date: Wed, 2 Oct 2024 14:49:52 -0700 Subject: [PATCH 18/28] subtree slide works with bft (no trait swaps through) --- .../bigfasttree/BigFastTreeModel.java | 22 +++++++++++++++++++ .../operators/SubtreeSlideOperator.java | 4 ++-- src/dr/evomodel/tree/TreeModel.java | 5 ++++- .../operators/SubtreeSlideOperatorParser.java | 8 +++++-- 4 files changed, 34 insertions(+), 5 deletions(-) diff --git a/src/dr/evomodel/bigfasttree/BigFastTreeModel.java b/src/dr/evomodel/bigfasttree/BigFastTreeModel.java index 2412cc8f92..b087a3bdf9 100644 --- a/src/dr/evomodel/bigfasttree/BigFastTreeModel.java +++ b/src/dr/evomodel/bigfasttree/BigFastTreeModel.java @@ -696,5 +696,27 @@ public Taxon getTaxon() { */ private final int internalNodeCount; + private boolean hasRates = false; + private boolean hasTraits = false; + + @Override + public boolean hasNodeTraits() { + // TODO Auto-generated method stub + return hasTraits; + } + + @Override + public void swapAllTraits(NodeRef node1, NodeRef node2) { + // TODO Auto-generated method stub + throw new UnsupportedOperationException("BFT model can not have traits! No trait to swap."); + } + + @Override + public boolean hasRates() { + // TODO Auto-generated method stub + return hasRates; + } + + } diff --git a/src/dr/evomodel/operators/SubtreeSlideOperator.java b/src/dr/evomodel/operators/SubtreeSlideOperator.java index c768d4321a..a1bfa54b86 100644 --- a/src/dr/evomodel/operators/SubtreeSlideOperator.java +++ b/src/dr/evomodel/operators/SubtreeSlideOperator.java @@ -48,7 +48,7 @@ public class SubtreeSlideOperator extends AbstractAdaptableTreeOperator { private static final boolean DEBUG = false; - private DefaultTreeModel tree = null; + private TreeModel tree = null; private double size = 1.0; private boolean gaussian = false; private final boolean swapInRandomRate; @@ -57,7 +57,7 @@ public class SubtreeSlideOperator extends AbstractAdaptableTreeOperator { private AdaptationMode mode = AdaptationMode.DEFAULT; private final double targetAcceptance; - public SubtreeSlideOperator(DefaultTreeModel tree, double weight, double size, boolean gaussian, + public SubtreeSlideOperator(TreeModel tree, double weight, double size, boolean gaussian, boolean swapRates, boolean swapTraits, boolean scaleDirichletBranches, AdaptationMode mode, double targetAcceptance) { super(mode, targetAcceptance); diff --git a/src/dr/evomodel/tree/TreeModel.java b/src/dr/evomodel/tree/TreeModel.java index 06b1cee47d..5557816ac0 100644 --- a/src/dr/evomodel/tree/TreeModel.java +++ b/src/dr/evomodel/tree/TreeModel.java @@ -262,7 +262,10 @@ public boolean hasNodeHeights() { public boolean hasBranchLengths() { return true; } - + abstract public boolean hasNodeTraits(); + abstract public void swapAllTraits(NodeRef node1, NodeRef node2); + abstract public boolean hasRates(); + public double getBranchLength(NodeRef node) { NodeRef parent = getParent(node); if (parent == null) { diff --git a/src/dr/evomodelxml/operators/SubtreeSlideOperatorParser.java b/src/dr/evomodelxml/operators/SubtreeSlideOperatorParser.java index 83982abe34..dd699cb387 100644 --- a/src/dr/evomodelxml/operators/SubtreeSlideOperatorParser.java +++ b/src/dr/evomodelxml/operators/SubtreeSlideOperatorParser.java @@ -27,8 +27,8 @@ package dr.evomodelxml.operators; +import dr.evomodel.bigfasttree.BigFastTreeModel; import dr.evomodel.operators.SubtreeSlideOperator; -import dr.evomodel.tree.DefaultTreeModel; import dr.evomodel.tree.TreeModel; import dr.inference.operators.AdaptableMCMCOperator; import dr.inference.operators.AdaptationMode; @@ -66,7 +66,11 @@ public Object parseXMLObject(XMLObject xo) throws XMLParseException { } } - DefaultTreeModel treeModel = (DefaultTreeModel) xo.getChild(DefaultTreeModel.class); + TreeModel treeModel = (TreeModel) xo.getChild(TreeModel.class); + + if((swapRates || swapTraits) && treeModel instanceof BigFastTreeModel) { + throw new XMLParseException("Swapping rates or traits is not implemented for BFT model yet."); + } final double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT); final double targetAcceptance = xo.getAttribute(TARGET_ACCEPTANCE, 0.234); From b42c7517e3e0a1ad5626bb11aa75190ad84ec54b Mon Sep 17 00:00:00 2001 From: jtmccr1 Date: Mon, 21 Oct 2024 13:08:59 -0500 Subject: [PATCH 19/28] forgot treemodel edits in constraints --- .../thorney/ConstrainedTreeModel.java | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/src/dr/evomodel/bigfasttree/thorney/ConstrainedTreeModel.java b/src/dr/evomodel/bigfasttree/thorney/ConstrainedTreeModel.java index 28a73b1ec8..7906cf6c90 100644 --- a/src/dr/evomodel/bigfasttree/thorney/ConstrainedTreeModel.java +++ b/src/dr/evomodel/bigfasttree/thorney/ConstrainedTreeModel.java @@ -1441,6 +1441,42 @@ public int getBaseNodeNumber() { public final int baseNodeNumber; } + + @Override + public boolean hasNodeTraits() { + // TODO Auto-generated method stub + throw new UnsupportedOperationException("Unimplemented method 'hasNodeTraits'"); + } + + @Override + public void swapAllTraits(NodeRef node1, NodeRef node2) { + // TODO Auto-generated method stub + throw new UnsupportedOperationException("Unimplemented method 'swapAllTraits'"); + } + + @Override + public boolean hasRates() { + // TODO Auto-generated method stub + throw new UnsupportedOperationException("Unimplemented method 'hasRates'"); + } + } + + @Override + public boolean hasNodeTraits() { + // TODO Auto-generated method stub + throw new UnsupportedOperationException("Unimplemented method 'hasNodeTraits'"); + } + + @Override + public void swapAllTraits(NodeRef node1, NodeRef node2) { + // TODO Auto-generated method stub + throw new UnsupportedOperationException("Unimplemented method 'swapAllTraits'"); + } + + @Override + public boolean hasRates() { + // TODO Auto-generated method stub + throw new UnsupportedOperationException("Unimplemented method 'hasRates'"); } } From a304f9b8f68b9b7502e7439b6684081be659d0a5 Mon Sep 17 00:00:00 2001 From: jtmccr1 Date: Mon, 21 Oct 2024 13:09:16 -0500 Subject: [PATCH 20/28] capitalization in rootheightproxy --- .../evomodel/bigfasttree/thorney/RootHeightProxyParameter.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/dr/evomodel/bigfasttree/thorney/RootHeightProxyParameter.java b/src/dr/evomodel/bigfasttree/thorney/RootHeightProxyParameter.java index 29eed5a0d7..72ab06e9dc 100644 --- a/src/dr/evomodel/bigfasttree/thorney/RootHeightProxyParameter.java +++ b/src/dr/evomodel/bigfasttree/thorney/RootHeightProxyParameter.java @@ -84,7 +84,7 @@ public void setParameterValueNotifyChangedAll(int dim, double value) { setParameterValue(dim, value); } - private static final String ROOT_HEIGHT_PARAMETER = "RootHeightProxyParameter"; + private static final String ROOT_HEIGHT_PARAMETER = "rootHeightProxyParameter"; public static AbstractXMLObjectParser PARSER = new AbstractXMLObjectParser() { @Override From 6fed2cbf4608f130ed53f29f3771c297d7800f15 Mon Sep 17 00:00:00 2001 From: jtmccr1 Date: Mon, 21 Oct 2024 14:48:29 -0500 Subject: [PATCH 21/28] adds bft to beauti jar --- build.xml | 1 + 1 file changed, 1 insertion(+) diff --git a/build.xml b/build.xml index fa6de05aea..0070951600 100644 --- a/build.xml +++ b/build.xml @@ -236,6 +236,7 @@ + From e6d89aa373608c8b59b28d305a20dc1f25291dd1 Mon Sep 17 00:00:00 2001 From: jtmccr1 Date: Tue, 19 Nov 2024 10:31:57 -0600 Subject: [PATCH 22/28] resolving AR conversations --- src/dr/app/beast/development_parsers.properties | 2 +- src/dr/app/beauti/options/PartitionClockModel.java | 6 ++---- src/dr/app/beauti/options/PartitionTreeModel.java | 4 ---- .../beauti/sitemodelspanel/PartitionModelPanel.java | 1 - .../operators/NodeHeightOperatorParser.java | 12 +----------- 5 files changed, 4 insertions(+), 21 deletions(-) diff --git a/src/dr/app/beast/development_parsers.properties b/src/dr/app/beast/development_parsers.properties index 6a978f15ec..0a31d62c07 100644 --- a/src/dr/app/beast/development_parsers.properties +++ b/src/dr/app/beast/development_parsers.properties @@ -1,7 +1,7 @@ # # development_parsers.properties # -# Copyright � 2002-2024 the BEAST Development Team +# Copyright © 2002-2024 the BEAST Development Team # http://beast.community/about # # This file is part of BEAST. diff --git a/src/dr/app/beauti/options/PartitionClockModel.java b/src/dr/app/beauti/options/PartitionClockModel.java index 3847109313..7079014a2b 100644 --- a/src/dr/app/beauti/options/PartitionClockModel.java +++ b/src/dr/app/beauti/options/PartitionClockModel.java @@ -557,7 +557,7 @@ public List selectOperators(List operators) { List ops = new ArrayList(); if (options.hasData()) { - // if (getDataType().getType() != DataType.TREE) { + if (getDataType().getType() != DataType.TREE || getPartitionTreeModel().isUsingThorneyBEAST()) { Operator rateOperator = getOperator("clock.rate"); switch (clockType) { @@ -670,13 +670,11 @@ public List selectOperators(List operators) { case AUTOCORRELATED: throw new UnsupportedOperationException("Autocorrelated clock not implemented yet"); -// break; - default: throw new IllegalArgumentException("Unknown clock model"); } - // } + } } Parameter allMuNus = getParameter(options.useNuRelativeRates() ? "allNus" : "allMus"); diff --git a/src/dr/app/beauti/options/PartitionTreeModel.java b/src/dr/app/beauti/options/PartitionTreeModel.java index 190e210fa6..c77e613263 100644 --- a/src/dr/app/beauti/options/PartitionTreeModel.java +++ b/src/dr/app/beauti/options/PartitionTreeModel.java @@ -27,7 +27,6 @@ package dr.app.beauti.options; -import dr.app.beauti.mcmcpanel.MCMCPanel; import dr.app.beauti.types.*; import dr.evolution.tree.Tree; @@ -194,9 +193,6 @@ public List selectParameters(List parameters) { // get parameter so their id prefix can be set. getParameter("tree"); - if(isUsingEmpiricalTrees()){ - return parameters; - } getParameter("treeModel.internalNodeHeights"); getParameter("treeModel.allInternalNodeHeights"); diff --git a/src/dr/app/beauti/sitemodelspanel/PartitionModelPanel.java b/src/dr/app/beauti/sitemodelspanel/PartitionModelPanel.java index 3381c8fb9a..5e036b9de9 100644 --- a/src/dr/app/beauti/sitemodelspanel/PartitionModelPanel.java +++ b/src/dr/app/beauti/sitemodelspanel/PartitionModelPanel.java @@ -40,7 +40,6 @@ import dr.app.beauti.types.FrequencyPolicyType; import dr.app.beauti.util.PanelUtils; import dr.app.gui.components.RealNumberField; -import dr.app.gui.components.WholeNumberField; import dr.app.util.OSType; import dr.evolution.datatype.DataType; import jam.panels.OptionsPanel; diff --git a/src/dr/evomodelxml/operators/NodeHeightOperatorParser.java b/src/dr/evomodelxml/operators/NodeHeightOperatorParser.java index 0618ef2072..9170304e01 100644 --- a/src/dr/evomodelxml/operators/NodeHeightOperatorParser.java +++ b/src/dr/evomodelxml/operators/NodeHeightOperatorParser.java @@ -48,9 +48,7 @@ public enum OperatorType { RANDOMWALK("random walk"), SCALEROOT("scale root"), SCALEALL("scale all internal"); -// MULTIMOVEUNIFORM("multiMoveUniform"); - // -JT the order in which nodes are picked matters but there is more than - // one way to pick the nodes I don't trust the multimove operator + OperatorType(String name) { this.name = name; @@ -107,12 +105,6 @@ public Object parseXMLObject(XMLObject xo) throws XMLParseException { throw new XMLParseException("The UniformNodeHeightOperator scaleFactor attribute must be between 0 and 1."); } } - // if (xo.hasAttribute(MEAN_COUNT)) { - // tuningParameter = xo.getDoubleAttribute(MEAN_COUNT); - // if (tuningParameter <= 0.0) { - // throw new XMLParseException("The UniformNodeHeightOperator nonshifted mean attribute must be positive and non-zero."); - // } - // } final double targetAcceptance = xo.getAttribute(TARGET_ACCEPTANCE, 0.234); @@ -126,8 +118,6 @@ public Object parseXMLObject(XMLObject xo) throws XMLParseException { case SCALEROOT: case SCALEALL: return new ScaleNodeHeightOperator(treeModel, weight, tuningParameter, operatorType, mode, targetAcceptance); -// case MULTIMOVEUNIFORM: -// return new MultiMoveUniformNodeHeightOperator(treeModel, weight, tuningParameter,mode,targetAcceptance); default: throw new IllegalArgumentException("Unknown operator type"); } From 8aed018bf4949289ec83ecb8e2453271db2cf351 Mon Sep 17 00:00:00 2001 From: jtmccr1 Date: Tue, 19 Nov 2024 11:35:08 -0600 Subject: [PATCH 23/28] updates bft and constrained tree to default xml --- .../beauti/generator/TreeModelGenerator.java | 52 +++--- .../bigfasttree/BigFastTreeModelParser.java | 172 ++++++------------ .../thorney/ConstrainedTreeModelParser.java | 67 ++++++- 3 files changed, 142 insertions(+), 149 deletions(-) diff --git a/src/dr/app/beauti/generator/TreeModelGenerator.java b/src/dr/app/beauti/generator/TreeModelGenerator.java index 3d1a4eaa10..92e811e438 100644 --- a/src/dr/app/beauti/generator/TreeModelGenerator.java +++ b/src/dr/app/beauti/generator/TreeModelGenerator.java @@ -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(XMLParser.ID, treeModelName + "." + TreeModelParser.ROOT_HEIGHT), true); + writer.writeCloseTag(TreeModelParser.ROOT_HEIGHT); + + writer.writeOpenTag(TreeModelParser.NODE_HEIGHTS, new Attribute.Default(TreeModelParser.INTERNAL_NODES, "true")); + writer.writeTag(ParameterParser.PARAMETER, + new Attribute.Default(XMLParser.ID, treeModelName + "." + "internalNodeHeights"), true); + writer.writeCloseTag(TreeModelParser.NODE_HEIGHTS); - writer.writeOpenTag(RootHeightProxyParameter.PARSER.getParserName(),new Attribute.Default(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(XMLParser.ID, treeModelName + "." + "internalNodeHeights"), - new Attribute.Default(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(XMLParser.ID, treeModelName + "." + "allInternalNodeHeights"), - new Attribute.Default(NodeHeightProxyParameter.INCLUDE_ROOT, "true") - }); - writer.writeIDref(ConstrainedTreeModelParser.CONSTRAINTS_TREE, treeModelName); + writer.writeOpenTag(TreeModelParser.NODE_HEIGHTS, + new Attribute[]{ + new Attribute.Default(TreeModelParser.INTERNAL_NODES, "true"), + new Attribute.Default(TreeModelParser.ROOT_NODE, "true") + }); + writer.writeTag(ParameterParser.PARAMETER, + new Attribute.Default(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); diff --git a/src/dr/evomodelxml/bigfasttree/BigFastTreeModelParser.java b/src/dr/evomodelxml/bigfasttree/BigFastTreeModelParser.java index c7e945fb3b..209a3e51af 100644 --- a/src/dr/evomodelxml/bigfasttree/BigFastTreeModelParser.java +++ b/src/dr/evomodelxml/bigfasttree/BigFastTreeModelParser.java @@ -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; @@ -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), }; } @@ -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; diff --git a/src/dr/evomodelxml/bigfasttree/thorney/ConstrainedTreeModelParser.java b/src/dr/evomodelxml/bigfasttree/thorney/ConstrainedTreeModelParser.java index 528aff5fa9..0b0cc37cbf 100644 --- a/src/dr/evomodelxml/bigfasttree/thorney/ConstrainedTreeModelParser.java +++ b/src/dr/evomodelxml/bigfasttree/thorney/ConstrainedTreeModelParser.java @@ -29,7 +29,13 @@ import dr.evolution.tree.Tree; import dr.evomodel.bigfasttree.thorney.ConstrainedTreeModel; +import dr.evomodel.bigfasttree.thorney.RootHeightProxyParameter; +import dr.evomodel.operators.RandomWalkIntegerNodeHeightWeightedOperator; import dr.evomodel.tree.TreeModel; +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; @@ -47,16 +53,59 @@ public Object parseXMLObject(XMLObject xo) throws XMLParseException { Tree tree = (Tree) xo.getChild(Tree.class); Tree constraintsTree = (Tree) xo.getElementFirstChild(CONSTRAINTS_TREE); - Logger.getLogger("dr.evomodel").info("\nCreating the constrained tree model based on big fast tree model, '" + xo.getId() + "'"); - ConstrainedTreeModel treeModel = new ConstrainedTreeModel(xo.getId(),tree, constraintsTree); + Logger.getLogger("dr.evomodel") + .info("\nCreating the constrained tree model based on big fast tree model, '" + xo.getId() + "'"); + ConstrainedTreeModel treeModel = new ConstrainedTreeModel(xo.getId(), tree, constraintsTree); Logger.getLogger("dr.evomodel").info(" taxon count = " + treeModel.getExternalNodeCount()); Logger.getLogger("dr.evomodel").info(" tree height = " + treeModel.getNodeHeight(treeModel.getRoot())); + + // 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 constrained 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 constrained 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 constrained trees"); + } + } + } + return treeModel; } - //************************************************************************ + // ************************************************************************ // AbstractXMLObjectParser implementation - //************************************************************************ + // ************************************************************************ public String getParserDescription() { return "This element represents the a tree model that with defined clades that may not be broken."; @@ -68,9 +117,17 @@ public Class getReturnType() { public static final XMLSyntaxRule[] rules = { new ElementRule(Tree.class), - new ElementRule(CONSTRAINTS_TREE, new XMLSyntaxRule[]{ + new ElementRule(CONSTRAINTS_TREE, new XMLSyntaxRule[] { new ElementRule(Tree.class) }), + 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), + }; public XMLSyntaxRule[] getSyntaxRules() { From f80a82b8ff7998449827d29aa37f5bd0aedc9ed0 Mon Sep 17 00:00:00 2001 From: jtmccr1 Date: Tue, 19 Nov 2024 13:40:31 -0600 Subject: [PATCH 24/28] removes duplication of empirical trees from tree panel --- src/dr/app/beauti/treespanel/PartitionTreeModelPanel.java | 1 - 1 file changed, 1 deletion(-) diff --git a/src/dr/app/beauti/treespanel/PartitionTreeModelPanel.java b/src/dr/app/beauti/treespanel/PartitionTreeModelPanel.java index 42bd51aae1..3c279ba03d 100644 --- a/src/dr/app/beauti/treespanel/PartitionTreeModelPanel.java +++ b/src/dr/app/beauti/treespanel/PartitionTreeModelPanel.java @@ -144,7 +144,6 @@ public PartitionTreeModelPanel(final BeautiFrame parent, PartitionTreeModel part for (TreeAsDataType treeAsDataType : TreeAsDataType.values()) { treeAsDataModelCombo.addItem(treeAsDataType); } - treeAsDataModelCombo.addItem(TreeAsDataType.EMPRICAL_TREES); PanelUtils.setupComponent(treeAsDataModelCombo); treeAsDataModelCombo.addItemListener(ev -> { this.partitionTreeModel.setTreeAsDataType((TreeAsDataType)treeAsDataModelCombo.getSelectedItem()); From e8a0c4302342e72e719e7cfd335cd524fb4adeeb Mon Sep 17 00:00:00 2001 From: jtmccr1 Date: Tue, 19 Nov 2024 13:42:01 -0600 Subject: [PATCH 25/28] adds warning for clock models without TB gradients --- .../app/beauti/generator/BeastGenerator.java | 17 ++++ .../beauti/options/PartitionTreeModel.java | 88 +++++++++++-------- 2 files changed, 66 insertions(+), 39 deletions(-) diff --git a/src/dr/app/beauti/generator/BeastGenerator.java b/src/dr/app/beauti/generator/BeastGenerator.java index 07f08a3603..41a0c05b6f 100644 --- a/src/dr/app/beauti/generator/BeastGenerator.java +++ b/src/dr/app/beauti/generator/BeastGenerator.java @@ -239,6 +239,23 @@ public void checkOptions() throws GeneratorException { } } + //+++++++++++++++++ ThorneyBEAST / clock model Verification ++++++++++++++ + + for (PartitionClockModel model : options.getPartitionClockModels()) { + for (AbstractPartitionData pd : options.getDataPartitions(model)) { + if(pd.getDataType().getType() ==DataType.TREE){ + PartitionTreeModel tm = pd.getPartitionTreeModel(); + if(tm.isUsingThorneyBEAST() && !PartitionTreeModel.thorneyCompatibleClocks.contains(model.getClockType())){ + throw new GeneratorException("Gradients for "+model.getClockType()+ + " are not implemented for Thorney BEAST." + + "Please use a clock model that does not rely on gradients.", BeautiFrame.CLOCK_MODELS); + + } + } + } + } + + //++++++++++++++++ Prior Bounds ++++++++++++++++++ for (Parameter param : options.selectParameters()) { if (!Double.isNaN(param.getInitial()) ) { diff --git a/src/dr/app/beauti/options/PartitionTreeModel.java b/src/dr/app/beauti/options/PartitionTreeModel.java index c77e613263..6b0be8056a 100644 --- a/src/dr/app/beauti/options/PartitionTreeModel.java +++ b/src/dr/app/beauti/options/PartitionTreeModel.java @@ -30,6 +30,7 @@ import dr.app.beauti.types.*; import dr.evolution.tree.Tree; +import java.util.Arrays; import java.util.List; /** @@ -56,8 +57,9 @@ public class PartitionTreeModel extends PartitionOptions { private boolean hasTipCalibrations = false; private boolean hasNodeCalibrations = false; - - + public static List thorneyCompatibleClocks = Arrays.asList( ClockType.STRICT_CLOCK, ClockType.UNCORRELATED, + ClockType.FIXED_LOCAL_CLOCK, ClockType.RANDOM_LOCAL_CLOCK, ClockType.FIXED_LOCAL_CLOCK, + ClockType.MIXED_EFFECTS_CLOCK ); private final TreePartitionData treePartitionData; @@ -97,23 +99,21 @@ public PartitionTreeModel(BeautiOptions options, String name, PartitionTreeModel userStartingTree = source.userStartingTree; isNewick = source.isNewick; -// initialRootHeight = source.initialRootHeight; + // initialRootHeight = source.initialRootHeight; initModelParametersAndOpererators(); } public void initModelParametersAndOpererators() { - - - createParameter("tree", "The tree"); createParameter("treeModel.internalNodeHeights", "internal node heights of the tree (except the root)"); createParameter("treeModel.allInternalNodeHeights", "internal node heights of the tree"); createParameterTree(this, "treeModel.rootHeight", "root height of the tree", true); if (treePartitionData == null) { - //TODO treeBitMove should move to PartitionClockModelTreeModelLink, after Alexei finish + // TODO treeBitMove should move to PartitionClockModelTreeModelLink, after + // Alexei finish createOperator("treeBitMove", "Tree", "Swaps the rates and change locations of local clocks", "tree", OperatorType.TREE_BIT_MOVE, -1.0, treeWeights); @@ -122,7 +122,9 @@ public void initModelParametersAndOpererators() { "treeModel.internalNodeHeights", OperatorType.UNIFORM, -1, branchWeights); // This scale operator is used instead of the up/down if the rate is fixed. - new Operator.Builder("treeModel.allInternalNodeHeights", "Scales all internal node heights in tree", getParameter("treeModel.allInternalNodeHeights"), OperatorType.SCALE_ALL, 0.75, rateWeights).build(operators); + new Operator.Builder("treeModel.allInternalNodeHeights", "Scales all internal node heights in tree", + getParameter("treeModel.allInternalNodeHeights"), OperatorType.SCALE_ALL, 0.75, rateWeights) + .build(operators); createOperator("subtreeSlide", "Tree", "Performs the subtree-slide rearrangement of the tree", "tree", OperatorType.SUBTREE_SLIDE, 1.0, treeWeights); @@ -141,17 +143,17 @@ public void initModelParametersAndOpererators() { createOperator("FHSPR", "Tree", "Performs the fixed-height subtree prune/regraft of the tree", "tree", OperatorType.FIXED_HEIGHT_SUBTREE_PRUNE_REGRAFT, 1.0, weight); } else { - //Thorney BEAST operators + // Thorney BEAST operators // Big weights operators double weight = Math.max(options.taxonList.getTaxonCount(), 30); - + // does STL works on constrained trees? createOperator("subtreeLeap", "Tree", "Performs the subtree-leap rearrangement of the tree", "tree", - OperatorType.SUBTREE_LEAP, 1.0, weight); - createOperator("uniformSPG", "Tree", "Performs the subtree prune regraft within a polytomony rearrangement of the tree", "tree", + OperatorType.SUBTREE_LEAP, 1.0, weight); + createOperator("uniformSPG", "Tree", + "Performs the subtree prune regraft within a polytomony rearrangement of the tree", "tree", OperatorType.UNIFORM_SUBTREE_PRUNE_REGRAFT, -1, weight); - createOperator("treeBitMove", "Tree", "Swaps the rates and change locations of local clocks", "tree", OperatorType.TREE_BIT_MOVE, -1.0, treeWeights); @@ -159,14 +161,18 @@ public void initModelParametersAndOpererators() { "treeModel.internalNodeHeights", OperatorType.UNIFORM, -1, weight); // This scale operator is used instead of the up/down if the rate is fixed. - new Operator.Builder("treeModel.allInternalNodeHeights", "Scales all internal node heights in tree", getParameter("treeModel.allInternalNodeHeights"), OperatorType.SCALE_ALL, 0.75, rateWeights).build(operators); + new Operator.Builder("treeModel.allInternalNodeHeights", "Scales all internal node heights in tree", + getParameter("treeModel.allInternalNodeHeights"), OperatorType.SCALE_ALL, 0.75, rateWeights) + .build(operators); - // In the TB setting this will almost always give the same likelihood since coalescent doesn't change + // In the TB setting this will almost always give the same likelihood since + // coalescent doesn't change // and if we are in the non mutation zone the treelikelihood will be the same. // not compatible with constrained tree right now. - // createOperator("FHSPR", "Tree", "Performs the fixed-height subtree prune/regraft of the tree", "tree", - // OperatorType.FIXED_HEIGHT_SUBTREE_PRUNE_REGRAFT, 1.0, weight); - + // createOperator("FHSPR", "Tree", "Performs the fixed-height subtree + // prune/regraft of the tree", "tree", + // OperatorType.FIXED_HEIGHT_SUBTREE_PRUNE_REGRAFT, 1.0, weight); + createOperator("narrowExchange", "Tree", "Performs local rearrangements of the tree", "tree", OperatorType.NARROW_EXCHANGE, -1, weight); @@ -176,9 +182,8 @@ public void initModelParametersAndOpererators() { createOperator("wideExchange", "Tree", "Performs global rearrangements of the tree", "tree", OperatorType.WIDE_EXCHANGE, -1, weight); - createOperator("wilsonBalding", "Tree", "Performs the Wilson-Balding rearrangement of the tree", "tree", - OperatorType.WILSON_BALDING, -1, weight); + OperatorType.WILSON_BALDING, -1, weight); } createOperator("empiricalTreeSwap", "Tree", "Sets the current tree from the empirical set", "tree", @@ -187,11 +192,12 @@ public void initModelParametersAndOpererators() { @Override public List selectParameters(List parameters) { -// setAvgRootAndRate(); + // setAvgRootAndRate(); - // Don't add these to the parameter list (as they don't appear in the table), but call + // Don't add these to the parameter list (as they don't appear in the table), + // but call // get parameter so their id prefix can be set. - + getParameter("tree"); getParameter("treeModel.internalNodeHeights"); getParameter("treeModel.allInternalNodeHeights"); @@ -212,11 +218,11 @@ public List selectParameters(List parameters) { @Override public List selectOperators(List operators) { -// setAvgRootAndRate(); + // setAvgRootAndRate(); if (isUsingEmpiricalTrees()) { operators.add(getOperator("empiricalTreeSwap")); - } else if(isUsingThorneyBEAST()){ + } else if (isUsingThorneyBEAST()) { operators.add(getOperator("treeModel.rootHeight")); operators.add(getOperator("uniformHeights")); @@ -225,10 +231,10 @@ public List selectOperators(List operators) { operators.add(getOperator("narrowExchange")); operators.add(getOperator("wideExchange")); operators.add(getOperator("wilsonBalding")); - //TODO add back in once operators is functional + // TODO add back in once operators is functional // operators.add(getOperator("FHSPR")); - }else { + } else { if (treePartitionData == null) { Operator subtreeSlideOp = getOperator("subtreeSlide"); if (!subtreeSlideOp.isTuningEdited()) { @@ -260,7 +266,7 @@ public List selectOperators(List operators) { // if not a fixed tree then sample tree space if (options.operatorSetType != OperatorSetType.FIXED_TREE) { if (options.operatorSetType == OperatorSetType.DEFAULT) { - newTreeOperatorsInUse = true; // default is now the new tree operators + newTreeOperatorsInUse = true; // default is now the new tree operators } else if (options.operatorSetType == OperatorSetType.CLASSIC) { defaultInUse = true; branchesInUse = true; @@ -324,6 +330,7 @@ public void setUserStartingTree(Tree userStartingTree) { public void setTreeAsDataType(TreeAsDataType treeAsDataType) { this.treeAsDataType = treeAsDataType; } + public TreeAsDataType getTreeAsDataType() { return treeAsDataType; } @@ -332,12 +339,14 @@ public boolean isUsingEmpiricalTrees() { return treePartitionData != null && treeAsDataType == TreeAsDataType.EMPRICAL_TREES; } - public boolean isUsingThorneyBEAST(){ + public boolean isUsingThorneyBEAST() { return treePartitionData != null && treeAsDataType == TreeAsDataType.THORNEY_BEAST; } + public void setUsingExternalEmpiricalTreeFile(boolean isUsingExternalEmpiricalTreeFile) { this.isUsingExternalEmpiricalTreeFile = isUsingExternalEmpiricalTreeFile; } + public boolean isUsingExternalEmpiricalTreeFile() { return isUsingExternalEmpiricalTreeFile; } @@ -356,7 +365,8 @@ public void setEmpiricalTreesFilename(String empiricalTreesFilename) { public double getThorneyScaler() { return thorneyScaler; } - public void setThorneyScaler(double scaler){ + + public void setThorneyScaler(double scaler) { this.thorneyScaler = scaler; } @@ -378,21 +388,21 @@ public boolean hasNodeCalibrations() { public double getInitialRootHeight() { return Double.NaN; -// return getAvgRootAndRate()[0]; + // return getAvgRootAndRate()[0]; } -// public void setInitialRootHeight(double initialRootHeight) { -// this.initialRootHeight = initialRootHeight; -// } + // public void setInitialRootHeight(double initialRootHeight) { + // this.initialRootHeight = initialRootHeight; + // } -// private void calculateInitialRootHeightPerTree() { -// initialRootHeight = options.clockModelOptions -// .calculateInitialRootHeightAndRate(options.getDataPartitions(this)) [0]; -// } + // private void calculateInitialRootHeightPerTree() { + // initialRootHeight = options.clockModelOptions + // .calculateInitialRootHeightAndRate(options.getDataPartitions(this)) [0]; + // } public String getPrefix() { String prefix = ""; - if (options.getPartitionTreeModels().size() > 1) { //|| options.isSpeciesAnalysis() + if (options.getPartitionTreeModels().size() > 1) { // || options.isSpeciesAnalysis() // There is more than one active partition model prefix += getName() + "."; } From 7d2bd2a6fea7f4afb7454a78c588e3f5cc3932d3 Mon Sep 17 00:00:00 2001 From: jtmccr1 Date: Tue, 19 Nov 2024 14:08:18 -0600 Subject: [PATCH 26/28] updating constrained tree xml in unit tests --- tests/TestXML/testCoalescentGradient.xml | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/tests/TestXML/testCoalescentGradient.xml b/tests/TestXML/testCoalescentGradient.xml index 3aa9c23c16..8f645578fa 100644 --- a/tests/TestXML/testCoalescentGradient.xml +++ b/tests/TestXML/testCoalescentGradient.xml @@ -3025,13 +3025,18 @@ + + + + + + + + + - - - - From 8226901805178ddc015b946b0dad58e5284fb4db Mon Sep 17 00:00:00 2001 From: jtmccr1 Date: Wed, 18 Dec 2024 09:21:03 -0600 Subject: [PATCH 27/28] Revert "thorney beast uses bft-intervals nows" This reverts commit 3661e1020aa52b1ed356017d14e86e8b0de3f614. --- .../beauti/generator/TreePriorGenerator.java | 77 ++++--------------- 1 file changed, 13 insertions(+), 64 deletions(-) diff --git a/src/dr/app/beauti/generator/TreePriorGenerator.java b/src/dr/app/beauti/generator/TreePriorGenerator.java index 04cf896ebf..f2423d0c4b 100644 --- a/src/dr/app/beauti/generator/TreePriorGenerator.java +++ b/src/dr/app/beauti/generator/TreePriorGenerator.java @@ -38,11 +38,10 @@ import dr.app.beauti.util.XMLWriter; import dr.evolution.util.Taxa; import dr.evolution.util.Units; -import dr.evomodel.bigfasttree.thorney.ConstrainedTreeModel; +import dr.evomodel.coalescent.GMRFSkyrideGradient; import dr.evomodel.tree.DefaultTreeModel; import dr.evomodelxml.coalescent.CoalescentLikelihoodParser; import dr.evomodelxml.coalescent.GMRFSkyrideGradientParser; -import dr.evomodelxml.bigfasttree.BigFastTreeIntervalsParser; import dr.evomodelxml.coalescent.GMRFSkyrideLikelihoodParser; import dr.evomodelxml.coalescent.demographicmodel.ConstantPopulationModelParser; import dr.evomodelxml.coalescent.demographicmodel.ExpansionModelParser; @@ -578,19 +577,9 @@ void writePriorLikelihood(PartitionTreeModel model, XMLWriter writer) { writeParameter(prior.getParameter("skyride.precision"), 1, writer); writer.writeCloseTag(GMRFSkyrideLikelihoodParser.PRECISION_PARAMETER); - - if(model.isUsingThorneyBEAST()){ - writer.writeOpenTag(GMRFSkyrideLikelihoodParser.INTERVALS); - writer.writeOpenTag(BigFastTreeIntervalsParser.TREE_INTERVALS); - writer.writeIDref(ConstrainedTreeModel.CONSTRAINED_TREE_MODEL, prefix + DefaultTreeModel.TREE_MODEL); - writer.writeCloseTag(BigFastTreeIntervalsParser.TREE_INTERVALS); - writer.writeCloseTag(GMRFSkyrideLikelihoodParser.INTERVALS); - }else{ - writer.writeOpenTag(GMRFSkyrideLikelihoodParser.POPULATION_TREE); - writer.writeIDref(DefaultTreeModel.TREE_MODEL, prefix + DefaultTreeModel.TREE_MODEL); - writer.writeCloseTag(GMRFSkyrideLikelihoodParser.POPULATION_TREE); - } - + writer.writeOpenTag(GMRFSkyrideLikelihoodParser.POPULATION_TREE); + writer.writeIDref(DefaultTreeModel.TREE_MODEL, prefix + DefaultTreeModel.TREE_MODEL); + writer.writeCloseTag(GMRFSkyrideLikelihoodParser.POPULATION_TREE); writer.writeCloseTag(GMRFSkyrideLikelihoodParser.SKYLINE_LIKELIHOOD); @@ -610,17 +599,9 @@ void writePriorLikelihood(PartitionTreeModel model, XMLWriter writer) { writer.writeOpenTag(CoalescentLikelihoodParser.MODEL); writeNodeHeightPriorModelRef(prior, writer); writer.writeCloseTag(CoalescentLikelihoodParser.MODEL); - if(model.isUsingThorneyBEAST()){ - writer.writeOpenTag(GMRFSkyrideLikelihoodParser.INTERVALS); - writer.writeOpenTag(BigFastTreeIntervalsParser.TREE_INTERVALS); - writer.writeIDref(ConstrainedTreeModel.CONSTRAINED_TREE_MODEL, prefix + DefaultTreeModel.TREE_MODEL); - writer.writeCloseTag(BigFastTreeIntervalsParser.TREE_INTERVALS); - writer.writeCloseTag(GMRFSkyrideLikelihoodParser.INTERVALS); - }else{ - writer.writeOpenTag(CoalescentLikelihoodParser.POPULATION_TREE); - writer.writeIDref(DefaultTreeModel.TREE_MODEL, prefix + DefaultTreeModel.TREE_MODEL); - writer.writeCloseTag(CoalescentLikelihoodParser.POPULATION_TREE); - } + writer.writeOpenTag(CoalescentLikelihoodParser.POPULATION_TREE); + writer.writeIDref(DefaultTreeModel.TREE_MODEL, prefix + DefaultTreeModel.TREE_MODEL); + writer.writeCloseTag(CoalescentLikelihoodParser.POPULATION_TREE); writer.writeCloseTag(CoalescentLikelihoodParser.COALESCENT_LIKELIHOOD); } } @@ -711,49 +692,17 @@ void writeMultiLociTreePriors(PartitionTreePrior prior, XMLWriter writer) { cutOff.setInitial(skyGridInterval); writeParameter(cutOff, 1, writer); writer.writeCloseTag(GMRFSkyrideLikelihoodParser.CUT_OFF); - + + writer.writeOpenTag(GMRFSkyrideLikelihoodParser.POPULATION_TREE); // TODO Add all linked trees if (options.isShareSameTreePrior()) { - Boolean usingTB=true; - for(PartitionTreeModel treeModel: options.getPartitionTreeModels()){ - if(!treeModel.isUsingThorneyBEAST()){ - usingTB=false; - break; - } - } - if(usingTB){ - writer.writeOpenTag(GMRFSkyrideLikelihoodParser.INTERVALS); - for (PartitionTreeModel thisModel : options.getPartitionTreeModels()) { - writer.writeOpenTag(BigFastTreeIntervalsParser.TREE_INTERVALS); - writer.writeIDref(ConstrainedTreeModel.CONSTRAINED_TREE_MODEL, thisModel.getPrefix() + DefaultTreeModel.TREE_MODEL); - writer.writeCloseTag(BigFastTreeIntervalsParser.TREE_INTERVALS); - } - writer.writeCloseTag(GMRFSkyrideLikelihoodParser.INTERVALS); - }else{ - writer.writeOpenTag(GMRFSkyrideLikelihoodParser.POPULATION_TREE); - for (PartitionTreeModel thisModel : options.getPartitionTreeModels()) { - writer.writeIDref(DefaultTreeModel.TREE_MODEL, thisModel.getPrefix() + DefaultTreeModel.TREE_MODEL); - } - writer.writeCloseTag(GMRFSkyrideLikelihoodParser.POPULATION_TREE); + for (PartitionTreeModel thisModel : options.getPartitionTreeModels()) { + writer.writeIDref(DefaultTreeModel.TREE_MODEL, thisModel.getPrefix() + DefaultTreeModel.TREE_MODEL); } } else { - - Boolean usingTB= options.getPartitionTreeModels(prior).get(0).isUsingThorneyBEAST(); - if(usingTB){ - writer.writeOpenTag(GMRFSkyrideLikelihoodParser.INTERVALS); - writer.writeOpenTag(BigFastTreeIntervalsParser.TREE_INTERVALS); - writer.writeIDref(ConstrainedTreeModel.CONSTRAINED_TREE_MODEL, options.getPartitionTreeModels(prior).get(0).getPrefix() + DefaultTreeModel.TREE_MODEL); - writer.writeCloseTag(BigFastTreeIntervalsParser.TREE_INTERVALS); - writer.writeCloseTag(GMRFSkyrideLikelihoodParser.INTERVALS); - - }else{ - writer.writeOpenTag(GMRFSkyrideLikelihoodParser.POPULATION_TREE); - writer.writeIDref(DefaultTreeModel.TREE_MODEL, options.getPartitionTreeModels(prior).get(0).getPrefix() + DefaultTreeModel.TREE_MODEL); - writer.writeCloseTag(GMRFSkyrideLikelihoodParser.POPULATION_TREE); - } + writer.writeIDref(DefaultTreeModel.TREE_MODEL, options.getPartitionTreeModels(prior).get(0).getPrefix() + DefaultTreeModel.TREE_MODEL); } - - + writer.writeCloseTag(GMRFSkyrideLikelihoodParser.POPULATION_TREE); writer.writeCloseTag(GMRFSkyrideLikelihoodParser.SKYGRID_LIKELIHOOD); From 41c40e7fe7f2fb813aca40a7946cf9b207c7d1e5 Mon Sep 17 00:00:00 2001 From: JT McCrone Date: Wed, 18 Dec 2024 09:09:04 -0800 Subject: [PATCH 28/28] reverting copyright sign --- src/dr/app/beast/development_parsers.properties | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/dr/app/beast/development_parsers.properties b/src/dr/app/beast/development_parsers.properties index 0a31d62c07..6a978f15ec 100644 --- a/src/dr/app/beast/development_parsers.properties +++ b/src/dr/app/beast/development_parsers.properties @@ -1,7 +1,7 @@ # # development_parsers.properties # -# Copyright © 2002-2024 the BEAST Development Team +# Copyright � 2002-2024 the BEAST Development Team # http://beast.community/about # # This file is part of BEAST.