Examples with TreeParameterModel dr.evomodel.tree.TreeParameterModel used on opensource projects

Example 1 with TreeParameterModel

use of dr.evomodel.tree.TreeParameterModel in project beast-mcmc by beast-dev.

the class BeastCheckpointer method readStateFromFile.

private long readStateFromFile(File file, MarkovChain markovChain, double[] lnL) {
    OperatorSchedule operatorSchedule = markovChain.getSchedule();
    long state = -1;
    ArrayList<TreeParameterModel> traitModels = new ArrayList<TreeParameterModel>();
    try {
        FileReader fileIn = new FileReader(file);
        BufferedReader in = new BufferedReader(fileIn);
        int[] rngState = null;
        String line = in.readLine();
        String[] fields = line.split("\t");
        if (fields[0].equals("rng")) {
            // if there is a random number generator state present then load it...
            try {
                rngState = new int[fields.length - 1];
                for (int i = 0; i < rngState.length; i++) {
                    rngState[i] = Integer.parseInt(fields[i + 1]);
                }
            } catch (NumberFormatException nfe) {
                throw new RuntimeException("Unable to read state number from state file");
            }
            line = in.readLine();
            fields = line.split("\t");
        }
        try {
            if (!fields[0].equals("state")) {
                throw new RuntimeException("Unable to read state number from state file");
            }
            state = Long.parseLong(fields[1]);
        } catch (NumberFormatException nfe) {
            throw new RuntimeException("Unable to read state number from state file");
        }
        line = in.readLine();
        fields = line.split("\t");
        try {
            if (!fields[0].equals("lnL")) {
                throw new RuntimeException("Unable to read lnL from state file");
            }
            if (lnL != null) {
                lnL[0] = Double.parseDouble(fields[1]);
            }
        } catch (NumberFormatException nfe) {
            throw new RuntimeException("Unable to read lnL from state file");
        }
        for (Parameter parameter : Parameter.CONNECTED_PARAMETER_SET) {
            line = in.readLine();
            fields = line.split("\t");
            //if (!fields[0].equals(parameter.getParameterName())) {
            //  System.err.println("Unable to match state parameter: " + fields[0] + ", expecting " + parameter.getParameterName());
            //}
            int dimension = Integer.parseInt(fields[2]);
            if (dimension != parameter.getDimension()) {
                System.err.println("Unable to match state parameter dimension: " + dimension + ", expecting " + parameter.getDimension() + " for parameter: " + parameter.getParameterName());
                System.err.print("Read from file: ");
                for (int i = 0; i < fields.length; i++) {
                    System.err.print(fields[i] + "\t");
                }
                System.err.println();
            }
            if (fields[1].equals("branchRates.categories.rootNodeNumber")) {
                // System.out.println("eek");
                double value = Double.parseDouble(fields[3]);
                parameter.setParameterValue(0, value);
                if (DEBUG) {
                    System.out.println("restoring " + fields[1] + " with value " + value);
                }
            } else {
                if (DEBUG) {
                    System.out.print("restoring " + fields[1] + " with values ");
                }
                for (int dim = 0; dim < parameter.getDimension(); dim++) {
                    parameter.setParameterValue(dim, Double.parseDouble(fields[dim + 3]));
                    if (DEBUG) {
                        System.out.print(Double.parseDouble(fields[dim + 3]) + " ");
                    }
                }
                if (DEBUG) {
                    System.out.println();
                }
            }
        }
        for (int i = 0; i < operatorSchedule.getOperatorCount(); i++) {
            MCMCOperator operator = operatorSchedule.getOperator(i);
            line = in.readLine();
            fields = line.split("\t");
            if (!fields[1].equals(operator.getOperatorName())) {
                throw new RuntimeException("Unable to match operator: " + fields[1]);
            }
            if (fields.length < 4) {
                throw new RuntimeException("Operator missing values: " + fields[1]);
            }
            operator.setAcceptCount(Integer.parseInt(fields[2]));
            operator.setRejectCount(Integer.parseInt(fields[3]));
            if (operator instanceof CoercableMCMCOperator) {
                if (fields.length != 5) {
                    throw new RuntimeException("Coercable operator missing parameter: " + fields[1]);
                }
                ((CoercableMCMCOperator) operator).setCoercableParameter(Double.parseDouble(fields[4]));
            }
        }
        // load the tree models last as we get the node heights from the tree (not the parameters which
        // which may not be associated with the right node
        Set<String> expectedTreeModelNames = new HashSet<String>();
        for (Model model : Model.CONNECTED_MODEL_SET) {
            if (model instanceof TreeModel) {
                if (DEBUG) {
                    System.out.println("model " + model.getModelName());
                }
                expectedTreeModelNames.add(model.getModelName());
                if (DEBUG) {
                    for (String s : expectedTreeModelNames) {
                        System.out.println(s);
                    }
                }
            }
            if (model instanceof TreeParameterModel) {
                traitModels.add((TreeParameterModel) model);
            }
        }
        line = in.readLine();
        fields = line.split("\t");
        // Read in all (possibly more than one) trees
        while (fields[0].equals("tree")) {
            if (DEBUG) {
                System.out.println("tree: " + fields[1]);
            }
            for (Model model : Model.CONNECTED_MODEL_SET) {
                if (model instanceof TreeModel && fields[1].equals(model.getModelName())) {
                    line = in.readLine();
                    line = in.readLine();
                    fields = line.split("\t");
                    //read number of nodes
                    int nodeCount = Integer.parseInt(fields[0]);
                    double[] nodeHeights = new double[nodeCount];
                    for (int i = 0; i < nodeCount; i++) {
                        line = in.readLine();
                        fields = line.split("\t");
                        nodeHeights[i] = Double.parseDouble(fields[1]);
                    }
                    //on to reading edge information
                    line = in.readLine();
                    line = in.readLine();
                    line = in.readLine();
                    fields = line.split("\t");
                    int edgeCount = Integer.parseInt(fields[0]);
                    //create data matrix of doubles to store information from list of TreeParameterModels
                    double[][] traitValues = new double[traitModels.size()][edgeCount];
                    //create array to store whether a node is left or right child of its parent
                    //can be important for certain tree transition kernels
                    int[] childOrder = new int[edgeCount];
                    for (int i = 0; i < childOrder.length; i++) {
                        childOrder[i] = -1;
                    }
                    int[] parents = new int[edgeCount];
                    for (int i = 0; i < edgeCount; i++) {
                        parents[i] = -1;
                    }
                    for (int i = 0; i < edgeCount; i++) {
                        line = in.readLine();
                        if (line != null) {
                            fields = line.split("\t");
                            parents[Integer.parseInt(fields[0])] = Integer.parseInt(fields[1]);
                            childOrder[i] = Integer.parseInt(fields[2]);
                            for (int j = 0; j < traitModels.size(); j++) {
                                traitValues[j][i] = Double.parseDouble(fields[3 + j]);
                            }
                        }
                    }
                    //perform magic with the acquired information
                    if (DEBUG) {
                        System.out.println("adopting tree structure");
                    }
                    //adopt the loaded tree structure; this does not yet copy the traits on the branches
                    ((TreeModel) model).beginTreeEdit();
                    ((TreeModel) model).adoptTreeStructure(parents, nodeHeights, childOrder);
                    ((TreeModel) model).endTreeEdit();
                    expectedTreeModelNames.remove(model.getModelName());
                }
            }
            line = in.readLine();
            if (line != null) {
                fields = line.split("\t");
            }
        }
        if (expectedTreeModelNames.size() > 0) {
            StringBuilder sb = new StringBuilder();
            for (String notFoundName : expectedTreeModelNames) {
                sb.append("Expecting, but unable to match state parameter:" + notFoundName + "\n");
            }
            throw new RuntimeException(sb.toString());
        }
        if (DEBUG) {
            System.out.println("\nDouble checking:");
            for (Parameter parameter : Parameter.CONNECTED_PARAMETER_SET) {
                if (parameter.getParameterName().equals("branchRates.categories.rootNodeNumber")) {
                    System.out.println(parameter.getParameterName() + ": " + parameter.getParameterValue(0));
                }
            }
        }
        if (rngState != null) {
            MathUtils.setRandomState(rngState);
        }
        in.close();
        fileIn.close();
    // This shouldn't be necessary and if it is then it might be hiding a bug...
    //            for (Likelihood likelihood : Likelihood.CONNECTED_LIKELIHOOD_SET) {
    //                likelihood.makeDirty();
    //            }
    } catch (IOException ioe) {
        throw new RuntimeException("Unable to read file: " + ioe.getMessage());
    }
    return state;
}

Example 2 with TreeParameterModel

use of dr.evomodel.tree.TreeParameterModel in project beast-mcmc by beast-dev.

the class BeastCheckpointer method writeStateToFile.

private boolean writeStateToFile(File file, long state, double lnL, MarkovChain markovChain) {
    OperatorSchedule operatorSchedule = markovChain.getSchedule();
    OutputStream fileOut = null;
    try {
        fileOut = new FileOutputStream(file);
        PrintStream out = new PrintStream(fileOut);
        ArrayList<TreeParameterModel> traitModels = new ArrayList<TreeParameterModel>();
        int[] rngState = MathUtils.getRandomState();
        out.print("rng");
        for (int i = 0; i < rngState.length; i++) {
            out.print("\t");
            out.print(rngState[i]);
        }
        out.println();
        out.print("state\t");
        out.println(state);
        out.print("lnL\t");
        out.println(lnL);
        for (Parameter parameter : Parameter.CONNECTED_PARAMETER_SET) {
            out.print("parameter");
            out.print("\t");
            out.print(parameter.getParameterName());
            out.print("\t");
            out.print(parameter.getDimension());
            for (int dim = 0; dim < parameter.getDimension(); dim++) {
                out.print("\t");
                out.print(parameter.getParameterValue(dim));
            }
            out.println();
        }
        for (int i = 0; i < operatorSchedule.getOperatorCount(); i++) {
            MCMCOperator operator = operatorSchedule.getOperator(i);
            out.print("operator");
            out.print("\t");
            out.print(operator.getOperatorName());
            out.print("\t");
            out.print(operator.getAcceptCount());
            out.print("\t");
            out.print(operator.getRejectCount());
            if (operator instanceof CoercableMCMCOperator) {
                out.print("\t");
                out.print(((CoercableMCMCOperator) operator).getCoercableParameter());
            }
            out.println();
        }
        //check up front if there are any TreeParameterModel objects
        for (Model model : Model.CONNECTED_MODEL_SET) {
            if (model instanceof TreeParameterModel) {
                //System.out.println("\nDetected TreeParameterModel: " + ((TreeParameterModel) model).toString());
                traitModels.add((TreeParameterModel) model);
            }
        }
        for (Model model : Model.CONNECTED_MODEL_SET) {
            if (model instanceof TreeModel) {
                out.print("tree");
                out.print("\t");
                out.println(model.getModelName());
                //replace Newick format by printing general graph structure
                //out.println(((TreeModel) model).getNewick());
                out.println("#node height taxon");
                int nodeCount = ((TreeModel) model).getNodeCount();
                out.println(nodeCount);
                for (int i = 0; i < nodeCount; i++) {
                    out.print(((TreeModel) model).getNode(i).getNumber());
                    out.print("\t");
                    out.print(((TreeModel) model).getNodeHeight(((TreeModel) model).getNode(i)));
                    if (((TreeModel) model).isExternal(((TreeModel) model).getNode(i))) {
                        out.print("\t");
                        out.print(((TreeModel) model).getNodeTaxon(((TreeModel) model).getNode(i)).getId());
                    }
                    out.println();
                }
                out.println("#edges");
                out.println("#child-node parent-node L/R-child traits");
                out.println(nodeCount);
                for (int i = 0; i < nodeCount; i++) {
                    NodeRef parent = ((TreeModel) model).getParent(((TreeModel) model).getNode(i));
                    if (parent != null) {
                        out.print(((TreeModel) model).getNode(i).getNumber());
                        out.print("\t");
                        out.print(((TreeModel) model).getParent(((TreeModel) model).getNode(i)).getNumber());
                        out.print("\t");
                        if ((((TreeModel) model).getChild(parent, 0) == ((TreeModel) model).getNode(i))) {
                            //left child
                            out.print(0);
                        } else if ((((TreeModel) model).getChild(parent, 1) == ((TreeModel) model).getNode(i))) {
                            //right child
                            out.print(1);
                        } else {
                            throw new RuntimeException("Operation currently only supported for nodes with 2 children.");
                        }
                        for (TreeParameterModel tpm : traitModels) {
                            out.print("\t");
                            out.print(tpm.getNodeValue((TreeModel) model, ((TreeModel) model).getNode(i)));
                        }
                        out.println();
                    }
                }
            }
        }
        out.close();
        fileOut.close();
    } catch (IOException ioe) {
        System.err.println("Unable to write file: " + ioe.getMessage());
        return false;
    }
    if (DEBUG) {
        for (Likelihood likelihood : Likelihood.CONNECTED_LIKELIHOOD_SET) {
            System.err.println(likelihood.getId() + ": " + likelihood.getLogLikelihood());
        }
    }
    return true;
}

Example 3 with TreeParameterModel

use of dr.evomodel.tree.TreeParameterModel in project beast-mcmc by beast-dev.

the class CheckPointModifier method readStateFromFile.

private long readStateFromFile(File file, MarkovChain markovChain, double[] lnL) {
    OperatorSchedule operatorSchedule = markovChain.getSchedule();
    long state = -1;
    this.traitModels = new ArrayList<TreeParameterModel>();
    try {
        FileReader fileIn = new FileReader(file);
        BufferedReader in = new BufferedReader(fileIn);
        int[] rngState = null;
        String line = in.readLine();
        String[] fields = line.split("\t");
        if (fields[0].equals("rng")) {
            // if there is a random number generator state present then load it...
            try {
                rngState = new int[fields.length - 1];
                for (int i = 0; i < rngState.length; i++) {
                    rngState[i] = Integer.parseInt(fields[i + 1]);
                }
            } catch (NumberFormatException nfe) {
                throw new RuntimeException("Unable to read state number from state file");
            }
            line = in.readLine();
            fields = line.split("\t");
        }
        try {
            if (!fields[0].equals("state")) {
                throw new RuntimeException("Unable to read state number from state file");
            }
            state = Long.parseLong(fields[1]);
        } catch (NumberFormatException nfe) {
            throw new RuntimeException("Unable to read state number from state file");
        }
        line = in.readLine();
        fields = line.split("\t");
        try {
            if (!fields[0].equals("lnL")) {
                throw new RuntimeException("Unable to read lnL from state file");
            }
            if (lnL != null) {
                lnL[0] = Double.parseDouble(fields[1]);
            }
        } catch (NumberFormatException nfe) {
            throw new RuntimeException("Unable to read lnL from state file");
        }
        line = in.readLine();
        //System.out.println(line);
        fields = line.split("\t");
        //Tree nodes have numbers as parameter ids
        for (Parameter parameter : Parameter.CONNECTED_PARAMETER_SET) {
            //numbers should be positive but can include zero
            if (isTreeNode(parameter.getId()) && isTreeNode(fields[1]) || parameter.getId().equals(fields[1])) {
                int dimension = Integer.parseInt(fields[2]);
                if (dimension != parameter.getDimension() && !fields[1].equals("branchRates.categories")) {
                    System.err.println("Unable to match state parameter dimension: " + dimension + ", expecting " + parameter.getDimension() + " for parameter: " + parameter.getParameterName());
                    System.err.print("Read from file: ");
                    for (int i = 0; i < fields.length; i++) {
                        System.err.print(fields[i] + "\t");
                    }
                    System.err.println();
                }
                if (fields[1].equals("branchRates.categories.rootNodeNumber")) {
                    // System.out.println("eek");
                    double value = Double.parseDouble(fields[3]);
                    parameter.setParameterValue(0, value);
                    if (DEBUG) {
                        System.out.println("restoring " + fields[1] + " with value " + value);
                    }
                } else {
                    if (DEBUG) {
                        System.out.print("restoring " + fields[1] + " with values ");
                    }
                    if (fields[1].equals("branchRates.categories")) {
                        for (int dim = 0; dim < (fields.length - 3); dim++) {
                            //System.out.println("dim " + dim);
                            parameter.setParameterValue(dim, Double.parseDouble(fields[dim + 3]));
                            if (DEBUG) {
                                System.out.print(Double.parseDouble(fields[dim + 3]) + " ");
                            }
                        }
                    } else {
                        for (int dim = 0; dim < parameter.getDimension(); dim++) {
                            parameter.setParameterValue(dim, Double.parseDouble(fields[dim + 3]));
                            if (DEBUG) {
                                System.out.print(Double.parseDouble(fields[dim + 3]) + " ");
                            }
                        }
                    }
                    if (DEBUG) {
                        System.out.println();
                    }
                }
                line = in.readLine();
                //System.out.println(line);
                fields = line.split("\t");
            } else {
            //there will be more parameters in the connected set than there are lines in the checkpoint file
            //do nothing and just keep iterating over the parameters in the connected set
            }
        }
        //No changes needed for loading in operators
        for (int i = 0; i < operatorSchedule.getOperatorCount(); i++) {
            MCMCOperator operator = operatorSchedule.getOperator(i);
            if (!fields[1].equals(operator.getOperatorName())) {
                throw new RuntimeException("Unable to match operator: " + fields[1]);
            }
            if (fields.length < 4) {
                throw new RuntimeException("Operator missing values: " + fields[1]);
            }
            operator.setAcceptCount(Integer.parseInt(fields[2]));
            operator.setRejectCount(Integer.parseInt(fields[3]));
            if (operator instanceof CoercableMCMCOperator) {
                if (fields.length != 5) {
                    throw new RuntimeException("Coercable operator missing parameter: " + fields[1]);
                }
                ((CoercableMCMCOperator) operator).setCoercableParameter(Double.parseDouble(fields[4]));
            }
            line = in.readLine();
            fields = line.split("\t");
        }
        // load the tree models last as we get the node heights from the tree (not the parameters which
        // which may not be associated with the right node
        Set<String> expectedTreeModelNames = new HashSet<String>();
        for (Model model : Model.CONNECTED_MODEL_SET) {
            if (model instanceof TreeModel) {
                expectedTreeModelNames.add(model.getModelName());
            }
            if (model instanceof TreeParameterModel) {
                this.traitModels.add((TreeParameterModel) model);
            }
            if (model instanceof BranchRates) {
                this.rateModel = (BranchRates) model;
            }
        }
        while (fields[0].equals("tree")) {
            for (Model model : Model.CONNECTED_MODEL_SET) {
                if (model instanceof TreeModel && fields[1].equals(model.getModelName())) {
                    //AR: Can we not just add them to a Flexible tree and then make a new TreeModel
                    //taking that in the constructor?
                    //internally, we have a tree with all the taxa
                    //externally, i.e. in the checkpoint file, we have a tree representation comprising
                    //a subset of the full taxa set
                    //write method that adjusts the internal representation, i.e. the one in the connected
                    //set, according to the checkpoint file and a distance-based approach to position
                    //the additional taxa
                    //first read in all the data from the checkpoint file
                    line = in.readLine();
                    line = in.readLine();
                    fields = line.split("\t");
                    //read number of nodes
                    int nodeCount = Integer.parseInt(fields[0]);
                    double[] nodeHeights = new double[nodeCount];
                    String[] taxaNames = new String[(nodeCount + 1) / 2];
                    for (int i = 0; i < nodeCount; i++) {
                        line = in.readLine();
                        fields = line.split("\t");
                        nodeHeights[i] = Double.parseDouble(fields[1]);
                        if (i < taxaNames.length) {
                            taxaNames[i] = fields[2];
                        }
                    }
                    //on to reading edge information
                    line = in.readLine();
                    line = in.readLine();
                    line = in.readLine();
                    fields = line.split("\t");
                    int edgeCount = Integer.parseInt(fields[0]);
                    //create data matrix of doubles to store information from list of TreeParameterModels
                    double[][] traitValues = new double[traitModels.size()][edgeCount];
                    //create array to store whether a node is left or right child of its parent
                    //can be important for certain tree transition kernels
                    int[] childOrder = new int[edgeCount];
                    for (int i = 0; i < childOrder.length; i++) {
                        childOrder[i] = -1;
                    }
                    int[] parents = new int[edgeCount];
                    for (int i = 0; i < edgeCount; i++) {
                        parents[i] = -1;
                    }
                    for (int i = 0; i < edgeCount; i++) {
                        line = in.readLine();
                        if (line != null) {
                            fields = line.split("\t");
                            parents[Integer.parseInt(fields[0])] = Integer.parseInt(fields[1]);
                            childOrder[i] = Integer.parseInt(fields[2]);
                            for (int j = 0; j < traitModels.size(); j++) {
                                traitValues[j][i] = Double.parseDouble(fields[3 + j]);
                            }
                        }
                    }
                    //perform magic with the acquired information
                    //CheckPointTreeModifier modifyTree = new CheckPointTreeModifier((TreeModel) model);
                    this.modifyTree = new CheckPointTreeModifier((TreeModel) model);
                    modifyTree.adoptTreeStructure(parents, nodeHeights, childOrder, taxaNames);
                    if (traitModels.size() > 0) {
                        modifyTree.adoptTraitData(parents, this.traitModels, traitValues);
                    }
                    //adopt the loaded tree structure; this does not yet copy the traits on the branches
                    //((TreeModel) model).beginTreeEdit();
                    //((TreeModel) model).adoptTreeStructure(parents, nodeHeights, childOrder);
                    //((TreeModel) model).endTreeEdit();
                    expectedTreeModelNames.remove(model.getModelName());
                }
            }
            line = in.readLine();
            if (line != null) {
                fields = line.split("\t");
            }
        }
        if (expectedTreeModelNames.size() > 0) {
            StringBuilder sb = new StringBuilder();
            for (String notFoundName : expectedTreeModelNames) {
                sb.append("Expecting, but unable to match state parameter:" + notFoundName + "\n");
            }
            throw new RuntimeException(sb.toString());
        }
        in.close();
        fileIn.close();
    } catch (IOException ioe) {
        throw new RuntimeException("Unable to read file: " + ioe.getMessage());
    }
    return state;
}

Example 4 with TreeParameterModel

use of dr.evomodel.tree.TreeParameterModel in project beast-mcmc by beast-dev.

the class CheckPointTreeModifier method interpolateTraitValues.

/**
     * The newly added taxa still need to be provided with trait values if there are any.
     * @param traitModels List of the trait models for which trait values need to be imputed / interpolated.
     */
public void interpolateTraitValues(ArrayList<TreeParameterModel> traitModels) {
    System.out.println();
    for (TreeParameterModel tpm : traitModels) {
        int numberOfInterpolations = 0;
        for (int i = 0; i < treeModel.getNodeCount(); i++) {
            if (tpm.getNodeValue(treeModel, treeModel.getNode(i)) == -1.0) {
                System.out.println("Current trait = -1.0 for node: " + treeModel.getNode(i));
                numberOfInterpolations++;
                double newValue = -1.0;
                //get trait value from sibling
                NodeRef parent = treeModel.getParent(treeModel.getNode(i));
                for (int j = 0; j < treeModel.getChildCount(parent); j++) {
                    NodeRef child = treeModel.getChild(parent, j);
                    if (tpm.getNodeValue(treeModel, child) != -1.0) {
                        tpm.setNodeValue(treeModel, treeModel.getNode(i), tpm.getNodeValue(treeModel, child) + 1.0);
                        System.out.println("Checking sibling trait.");
                        System.out.println("Setting node trait for node " + treeModel.getNode(i) + " to " + tpm.getNodeValue(treeModel, treeModel.getNode(i)));
                        break;
                    }
                }
                //if not successful, get trait from its parent
                if (tpm.getNodeValue(treeModel, treeModel.getNode(i)) == -1.0) {
                    NodeRef currentNode = treeModel.getNode(i);
                    //TODO Check for situations where no proper trait can be found
                    while (currentNode != treeModel.getRoot() && tpm.getNodeValue(treeModel, currentNode) == -1.0) {
                        currentNode = treeModel.getParent(currentNode);
                    }
                    tpm.setNodeValue(treeModel, treeModel.getNode(i), tpm.getNodeValue(treeModel, currentNode) + 1.0);
                    System.out.println("Checking parent trait.");
                    System.out.println("Setting node trait for node " + treeModel.getNode(i) + " to " + tpm.getNodeValue(treeModel, currentNode));
                }
                //adjust the other trait values after a trait has been imputed
                for (int j = 0; j < treeModel.getNodeCount(); j++) {
                    if (treeModel.getNode(j) != treeModel.getNode(i)) {
                        if (tpm.getNodeValue(treeModel, treeModel.getNode(j)) >= tpm.getNodeValue(treeModel, treeModel.getNode(i))) {
                            System.out.print("Updating trait from " + tpm.getNodeValue(treeModel, treeModel.getNode(j)));
                            tpm.setNodeValue(treeModel, treeModel.getNode(j), tpm.getNodeValue(treeModel, treeModel.getNode(j)) + 1.0);
                            System.out.println(" to " + tpm.getNodeValue(treeModel, treeModel.getNode(j)));
                        }
                    }
                }
            }
        /*if (tpm.getNodeValue(treeModel, treeModel.getNode(i)) == -1.0) {
                    for (int j = 0; j < treeModel.getNodeCount(); j++) {
                        if (treeModel.getNode(j) != treeModel.getNode(i)) {
                            if (tpm.getNodeValue(treeModel, treeModel.getNode(j)) >= tpm.getNodeValue(treeModel, treeModel.getNode(i))) {
                                System.out.print("Updating trait from " + tpm.getNodeValue(treeModel, treeModel.getNode(j)));
                                tpm.setNodeValue(treeModel, treeModel.getNode(j), tpm.getNodeValue(treeModel, treeModel.getNode(j)) + 1.0);
                                System.out.println(" to " + tpm.getNodeValue(treeModel, treeModel.getNode(j)));
                            }
                        }
                    }
                }*/
        }
        System.out.println("Number of interpolations: " + numberOfInterpolations);
    }
    System.out.println("Done.\n");
}

Example 5 with TreeParameterModel

use of dr.evomodel.tree.TreeParameterModel in project beast-mcmc by beast-dev.

the class CheckPointTreeModifier method adoptTraitData.

/**
     * Imports trait information from a file
     * @param edges Edges are provided as index: child number; parent: array entry
     * @param traitModels List of TreeParameterModel object that contain trait information
     * @param traitValues Values to be copied into the List of TreeParameterModel objects
     */
//TODO Small difference in reconstructed log likelihood, probably due to increased number of rate categories
public void adoptTraitData(int[] edges, ArrayList<TreeParameterModel> traitModels, double[][] traitValues) {
    int index = 0;
    for (TreeParameterModel tpm : traitModels) {
        int k = 0;
        for (int i = 0; i < edges.length; i++) {
            System.out.println(i + "   " + edges[i]);
            if (edges[i] != -1) {
                //TODO Seems like I messed up here
                if (i < (treeModel.getExternalNodeCount() - additionalTaxa)) {
                    tpm.setNodeValue(this.treeModel, this.treeModel.getExternalNode(nodeMap[i]), traitValues[index][k]);
                    System.out.println("Setting external node " + this.treeModel.getExternalNode(nodeMap[i]) + " to " + traitValues[index][k]);
                } else {
                    tpm.setNodeValue(this.treeModel, this.treeModel.getNode(i + additionalTaxa), traitValues[index][k]);
                    System.out.println("Setting internal node " + this.treeModel.getNode(i + additionalTaxa) + " to " + traitValues[index][k]);
                }
            } else {
                k--;
            }
            k++;
        }
        //set trait of remaining internal nodes to -1.0
        for (int i = 0; i < additionalTaxa; i++) {
            tpm.setNodeValue(this.treeModel, treeModel.getNode(treeModel.getNodeCount() - 1 - i), -1.0);
        }
        //set trait of newly added external taxa to -1.0
        int shift = 0;
        for (int i = 0; i < (treeModel.getExternalNodeCount() - additionalTaxa); i++) {
            System.out.println("i = " + i + " ; nodeMap[i] = " + nodeMap[i]);
        }
        System.out.println();
        for (String name : newTaxaNames) {
            System.out.println("new taxon: " + name);
        }
        int externalMissing = 0;
        for (String name : newTaxaNames) {
            for (int i = 0; i < treeModel.getExternalNodeCount(); i++) {
                if (treeModel.getNodeTaxon(treeModel.getExternalNode(i)).getId().equals(name)) {
                    externalMissing++;
                    tpm.setNodeValue(this.treeModel, this.treeModel.getExternalNode(i), -1.0);
                }
            }
        }
        System.out.println("External nodes with trait set to -1.0 = " + externalMissing + "\n");
    /*for (int i = 0; i < (treeModel.getExternalNodeCount()-additionalTaxa); i++) {
                System.out.println("i = " + i + " ; nodeMap[i] = " + nodeMap[i]);
                if (i != (nodeMap[i]-shift)) {
                    int difference = nodeMap[i] - i;
                    shift = difference;
                    tpm.setNodeValue(this.treeModel, this.treeModel.getExternalNode(nodeMap[i]-1), -1.0);
                    System.out.println("Setting external node: " + (nodeMap[i]-1));
                    externalMissing++;
                }
            }
            System.out.println("External node with trait set to -1.0 = " + externalMissing);
            index++;*/
    }
}