Examples with SubstitutionModel dr.evomodel.substmodel.SubstitutionModel used on opensource projects

Example 6 with SubstitutionModel

use of dr.evomodel.substmodel.SubstitutionModel in project beast-mcmc by beast-dev.

the class BranchAssignmentModelParser method parseXMLObject.

@Override
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Logger.getLogger("dr.evomodel").info("\nUsing branch assignment branch model.");
    TreeModel treeModel = (TreeModel) xo.getChild(TreeModel.class);
    String annotation = xo.getStringAttribute(ANNOTATION);
    LinkedHashMap<Integer, SubstitutionModel> modelIndexMap = new LinkedHashMap<Integer, SubstitutionModel>();
    for (int i = 0; i < xo.getChildCount(); i++) {
        if (xo.getChild(i) instanceof XMLObject) {
            XMLObject xoc = (XMLObject) xo.getChild(i);
            if (xoc.getName().equals(ASSIGNMENT)) {
                Integer index = null;
                if (xoc.hasAttribute(ANNOTATION_VALUE)) {
                    index = xoc.getIntegerAttribute(ANNOTATION_VALUE);
                }
                SubstitutionModel model = (SubstitutionModel) xoc.getChild(SubstitutionModel.class);
                modelIndexMap.put(index, model);
            }
        }
    }
    SubstitutionModel baseModel = (SubstitutionModel) xo.getElementFirstChild(BASE_MODEL);
    return new BranchAssignmentModel(treeModel, annotation, modelIndexMap, baseModel);
}

Example 7 with SubstitutionModel

use of dr.evomodel.substmodel.SubstitutionModel in project beast-mcmc by beast-dev.

the class MarkovJumpsBeagleTreeLikelihood method addRegister.

public void addRegister(Parameter addRegisterParameter, MarkovJumpsType type, boolean scaleByTime) {
    if ((type == MarkovJumpsType.COUNTS && addRegisterParameter.getDimension() != stateCount * stateCount) || (type == MarkovJumpsType.REWARDS && addRegisterParameter.getDimension() != stateCount)) {
        throw new RuntimeException("Register parameter of wrong dimension");
    }
    addVariable(addRegisterParameter);
    final String tag = addRegisterParameter.getId();
    for (int i = 0; i < substitutionModelDelegate.getSubstitutionModelCount(); ++i) {
        boolean isEpochModel = branchModel instanceof EpochBranchModel;
        registerParameter.add(addRegisterParameter);
        MarkovJumpsSubstitutionModel mjModel;
        SubstitutionModel substitutionModel = substitutionModelDelegate.getSubstitutionModel(i);
        if (useUniformization) {
            mjModel = new UniformizedSubstitutionModel(substitutionModel, type, nSimulants);
        } else {
            if (type == MarkovJumpsType.HISTORY) {
                throw new RuntimeException("Can only report complete history using uniformization");
            }
            mjModel = new MarkovJumpsSubstitutionModel(substitutionModel, type);
        }
        markovjumps.add(mjModel);
        branchModelNumber.add(i);
        addModel(mjModel);
        setupRegistration(numRegisters);
        String traitName;
        if (substitutionModelDelegate.getSubstitutionModelCount() == 1) {
            traitName = tag;
        } else {
            traitName = tag + i;
        }
        jumpTag.add(traitName);
        expectedJumps.add(new double[treeModel.getNodeCount()][patternCount]);
        // storedExpectedJumps.add(new double[treeModel.getNodeCount()][patternCount]);
        boolean[] oldScaleByTime = this.scaleByTime;
        int oldScaleByTimeLength = (oldScaleByTime == null ? 0 : oldScaleByTime.length);
        this.scaleByTime = new boolean[oldScaleByTimeLength + 1];
        if (oldScaleByTimeLength > 0) {
            System.arraycopy(oldScaleByTime, 0, this.scaleByTime, 0, oldScaleByTimeLength);
        }
        this.scaleByTime[oldScaleByTimeLength] = scaleByTime;
        if (type != MarkovJumpsType.HISTORY) {
            TreeTrait.DA da = new TreeTrait.DA() {

                final int registerNumber = numRegisters;

                public String getTraitName() {
                    return tag;
                }

                public Intent getIntent() {
                    return Intent.BRANCH;
                }

                public double[] getTrait(Tree tree, NodeRef node) {
                    return getMarkovJumpsForNodeAndRegister(tree, node, registerNumber);
                }
            };
            treeTraits.addTrait(traitName + "_base", da);
            treeTraits.addTrait(addRegisterParameter.getId(), new TreeTrait.SumAcrossArrayD(new TreeTrait.SumOverTreeDA(da)));
        } else {
            if (i == 0 || !isEpochModel) {
                if (histories == null) {
                    histories = new String[treeModel.getNodeCount()][patternCount];
                } else {
                    throw new RuntimeException("Only one complete history per markovJumpTreeLikelihood is allowed");
                }
                if (nSimulants > 1) {
                    throw new RuntimeException("Only one simulant allowed when saving complete history");
                }
                // Add total number of changes over tree trait
                TreeTrait da = new TreeTrait.DA() {

                    final int registerNumber = numRegisters;

                    public String getTraitName() {
                        return tag;
                    }

                    public Intent getIntent() {
                        return Intent.BRANCH;
                    }

                    public double[] getTrait(Tree tree, NodeRef node) {
                        return getMarkovJumpsForNodeAndRegister(tree, node, registerNumber);
                    }
                };
                treeTraits.addTrait(addRegisterParameter.getId(), new TreeTrait.SumOverTreeDA(da));
                // Record the complete history for this register
                historyRegisterNumber = numRegisters;
                ((UniformizedSubstitutionModel) mjModel).setSaveCompleteHistory(true);
                if (useCompactHistory && logHistory) {
                    treeTraits.addTrait(ALL_HISTORY, new TreeTrait.SA() {

                        public String getTraitName() {
                            return ALL_HISTORY;
                        }

                        public Intent getIntent() {
                            return Intent.BRANCH;
                        }

                        public boolean getFormatAsArray() {
                            return true;
                        }

                        public String[] getTrait(Tree tree, NodeRef node) {
                            List<String> events = new ArrayList<String>();
                            for (int i = 0; i < patternCount; i++) {
                                String eventString = getHistoryForNode(tree, node, i);
                                if (eventString != null && eventString.compareTo("{}") != 0) {
                                    eventString = eventString.substring(1, eventString.length() - 1);
                                    if (eventString.contains("},{")) {
                                        // There are multiple events
                                        String[] elements = eventString.split("(?<=\\}),(?=\\{)");
                                        for (String e : elements) {
                                            events.add(e);
                                        }
                                    } else {
                                        events.add(eventString);
                                    }
                                }
                            }
                            String[] array = new String[events.size()];
                            events.toArray(array);
                            return array;
                        }

                        public boolean getLoggable() {
                            return true;
                        }
                    });
                }
                for (int site = 0; site < patternCount; ++site) {
                    final String anonName = (patternCount == 1) ? HISTORY : HISTORY + "_" + (site + 1);
                    final int anonSite = site;
                    treeTraits.addTrait(anonName, new TreeTrait.S() {

                        public String getTraitName() {
                            return anonName;
                        }

                        public Intent getIntent() {
                            return Intent.BRANCH;
                        }

                        public String getTrait(Tree tree, NodeRef node) {
                            String history = getHistoryForNode(tree, node, anonSite);
                            // Return null if empty
                            return (history.compareTo("{}") != 0) ? history : null;
                        }

                        public boolean getLoggable() {
                            return logHistory && !useCompactHistory;
                        }
                    });
                }
            }
            if (isEpochModel) {
                for (int j = 0; j < markovjumps.size(); ++j) {
                    ((UniformizedSubstitutionModel) markovjumps.get(j)).setSaveCompleteHistory(true);
                }
            }
        }
        numRegisters++;
    }
// End of loop over branch models
}

Example 8 with SubstitutionModel

use of dr.evomodel.substmodel.SubstitutionModel in project beast-mcmc by beast-dev.

the class BranchSpecificBranchModelParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Logger.getLogger("dr.evomodel").info("\nUsing clade-specific branch model.");
    TreeModel tree = (TreeModel) xo.getChild(TreeModel.class);
    SubstitutionModel substitutionModel = (SubstitutionModel) xo.getChild(SubstitutionModel.class);
    BranchSpecificBranchModel branchModel = new BranchSpecificBranchModel(tree, substitutionModel);
    for (int i = 0; i < xo.getChildCount(); i++) {
        if (xo.getChild(i) instanceof XMLObject) {
            XMLObject xoc = (XMLObject) xo.getChild(i);
            if (xoc.getName().equals(CLADE)) {
                double stemWeight = xoc.getAttribute(STEM_WEIGHT, 0.0);
                substitutionModel = (SubstitutionModel) xoc.getChild(SubstitutionModel.class);
                TaxonList taxonList = (TaxonList) xoc.getChild(TaxonList.class);
                if (taxonList.getTaxonCount() == 1) {
                    throw new XMLParseException("A clade must be defined by at least two taxa");
                }
                try {
                    branchModel.addClade(taxonList, substitutionModel, stemWeight);
                } catch (TreeUtils.MissingTaxonException mte) {
                    throw new XMLParseException("Taxon, " + mte + ", in " + getParserName() + " was not found in the tree.");
                }
            } else if (xoc.getName().equals(EXTERNAL_BRANCHES)) {
                substitutionModel = (SubstitutionModel) xoc.getChild(SubstitutionModel.class);
                TaxonList taxonList = (TaxonList) xoc.getChild(TaxonList.class);
                try {
                    branchModel.addExternalBranches(taxonList, substitutionModel);
                } catch (TreeUtils.MissingTaxonException mte) {
                    throw new XMLParseException("Taxon, " + mte + ", in " + getParserName() + " was not found in the tree.");
                }
            } else if (xoc.getName().equals(BACKBONE)) {
                substitutionModel = (SubstitutionModel) xoc.getChild(SubstitutionModel.class);
                TaxonList taxonList = (TaxonList) xoc.getChild(TaxonList.class);
                try {
                    branchModel.addBackbone(taxonList, substitutionModel);
                } catch (TreeUtils.MissingTaxonException mte) {
                    throw new XMLParseException("Taxon, " + mte + ", in " + getParserName() + " was not found in the tree.");
                }
            }
        }
    }
    return branchModel;
}

Example 9 with SubstitutionModel

use of dr.evomodel.substmodel.SubstitutionModel in project beast-mcmc by beast-dev.

the class ExternalInternalBranchModelParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Logger.getLogger("dr.evomodel").info("\nUsing external-internal branch model.");
    TreeModel tree = (TreeModel) xo.getChild(TreeModel.class);
    SubstitutionModel internalSubstitutionModel = (SubstitutionModel) xo.getChild(SubstitutionModel.class);
    SubstitutionModel externalSubstitutionModel = (SubstitutionModel) xo.getElementFirstChild(EXTERNAL_BRANCHES);
    return new ExternalInternalBranchModel(tree, externalSubstitutionModel, internalSubstitutionModel);
}

Example 10 with SubstitutionModel

use of dr.evomodel.substmodel.SubstitutionModel in project beast-mcmc by beast-dev.

the class RandomBranchAssignmentModelParser method parseXMLObject.

@Override
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Logger.getLogger("dr.evomodel").info("\nUsing random assignment branch model.");
    TreeModel treeModel = (TreeModel) xo.getChild(TreeModel.class);
    XMLObject cxo = xo.getChild(MODELS);
    List<SubstitutionModel> substitutionModels = new ArrayList<SubstitutionModel>();
    for (int i = 0; i < cxo.getChildCount(); i++) {
        SubstitutionModel substModel = (SubstitutionModel) cxo.getChild(i);
        substitutionModels.add(substModel);
    }
    return new RandomBranchAssignmentModel(treeModel, substitutionModels);
}