Examples with CoercableMCMCOperator dr.inference.operators.CoercableMCMCOperator used on opensource projects

Example 1 with CoercableMCMCOperator

use of dr.inference.operators.CoercableMCMCOperator 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 CoercableMCMCOperator

use of dr.inference.operators.CoercableMCMCOperator 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 CoercableMCMCOperator

use of dr.inference.operators.CoercableMCMCOperator in project beast-mcmc by beast-dev.

the class MCMCMC method finish.

/**
     * cleans up when the chain finishes (possibly early).
     */
private void finish() {
    NumberFormatter formatter = new NumberFormatter(8);
    MCLogger[] loggers = mcLoggers[coldChain];
    for (MCLogger logger : loggers) {
        logger.log(currentState);
        logger.stopLogging();
    }
    System.out.println();
    System.out.println("Time taken: " + timer.toString());
    if (showOperatorAnalysis) {
        System.out.println();
        System.out.println("Operator analysis");
        System.out.println(formatter.formatToFieldWidth("Operator", 30) + formatter.formatToFieldWidth("", 8) + formatter.formatToFieldWidth("Pr(accept)", 11) + " Performance suggestion");
        for (int i = 0; i < schedules[coldChain].getOperatorCount(); i++) {
            MCMCOperator op = schedules[coldChain].getOperator(i);
            double acceptanceProb = MCMCOperator.Utils.getAcceptanceProbability(op);
            String message = "good";
            if (acceptanceProb < op.getMinimumGoodAcceptanceLevel()) {
                if (acceptanceProb < (op.getMinimumAcceptanceLevel() / 10.0)) {
                    message = "very low";
                } else if (acceptanceProb < op.getMinimumAcceptanceLevel()) {
                    message = "low";
                } else
                    message = "slightly low";
            } else if (acceptanceProb > op.getMaximumGoodAcceptanceLevel()) {
                double reallyHigh = 1.0 - ((1.0 - op.getMaximumAcceptanceLevel()) / 10.0);
                if (acceptanceProb > reallyHigh) {
                    message = "very high";
                } else if (acceptanceProb > op.getMaximumAcceptanceLevel()) {
                    message = "high";
                } else
                    message = "slightly high";
            }
            String suggestion = op.getPerformanceSuggestion();
            String pString = "        ";
            if (op instanceof CoercableMCMCOperator) {
                pString = formatter.formatToFieldWidth(formatter.formatDecimal(((CoercableMCMCOperator) op).getRawParameter(), 3), 8);
            }
            System.out.println(formatter.formatToFieldWidth(op.getOperatorName(), 30) + pString + formatter.formatToFieldWidth(formatter.formatDecimal(acceptanceProb, 4), 11) + " " + message + "\t" + suggestion);
        }
        System.out.println();
    }
}

Example 4 with CoercableMCMCOperator

use of dr.inference.operators.CoercableMCMCOperator in project beast-mcmc by beast-dev.

the class MCMCMC method swapChainTemperatures.

private int swapChainTemperatures() {
    if (DEBUG) {
        System.out.print("Current scores: ");
        for (int i = 0; i < chains.length; i++) {
            System.out.print("\t");
            if (i == coldChain) {
                System.out.print("[");
            }
            System.out.print(chains[i].getCurrentScore());
            if (i == coldChain) {
                System.out.print("]");
            }
        }
        System.out.println();
    }
    int newColdChain = coldChain;
    int index1 = MathUtils.nextInt(chains.length);
    int index2 = MathUtils.nextInt(chains.length);
    while (index1 == index2) {
        index2 = MathUtils.nextInt(chains.length);
    }
    double score1 = chains[index1].getCurrentScore();
    MCMCCriterion acceptor1 = ((MCMCCriterion) chains[index1].getAcceptor());
    double temperature1 = acceptor1.getTemperature();
    double score2 = chains[index2].getCurrentScore();
    MCMCCriterion acceptor2 = ((MCMCCriterion) chains[index2].getAcceptor());
    double temperature2 = acceptor2.getTemperature();
    double logRatio = ((score2 - score1) * temperature1) + ((score1 - score2) * temperature2);
    boolean swap = (Math.log(MathUtils.nextDouble()) < logRatio);
    if (swap) {
        if (DEBUG) {
            System.out.println("Swapping chain " + index1 + " and chain " + index2);
        }
        acceptor1.setTemperature(temperature2);
        acceptor2.setTemperature(temperature1);
        OperatorSchedule schedule1 = schedules[index1];
        OperatorSchedule schedule2 = schedules[index2];
        for (int i = 0; i < schedule1.getOperatorCount(); i++) {
            MCMCOperator operator1 = schedule1.getOperator(i);
            MCMCOperator operator2 = schedule2.getOperator(i);
            long tmp = operator1.getAcceptCount();
            operator1.setAcceptCount(operator2.getAcceptCount());
            operator2.setAcceptCount(tmp);
            tmp = operator1.getRejectCount();
            operator1.setRejectCount(operator2.getRejectCount());
            operator2.setRejectCount(tmp);
            double tmp2 = operator1.getSumDeviation();
            operator1.setSumDeviation(operator2.getSumDeviation());
            operator2.setSumDeviation(tmp2);
            if (operator1 instanceof CoercableMCMCOperator) {
                tmp2 = ((CoercableMCMCOperator) operator1).getCoercableParameter();
                ((CoercableMCMCOperator) operator1).setCoercableParameter(((CoercableMCMCOperator) operator2).getCoercableParameter());
                ((CoercableMCMCOperator) operator2).setCoercableParameter(tmp2);
            }
        }
        if (index1 == coldChain) {
            newColdChain = index2;
        } else if (index2 == coldChain) {
            newColdChain = index1;
        }
    }
    return newColdChain;
}

Example 5 with CoercableMCMCOperator

use of dr.inference.operators.CoercableMCMCOperator 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;
}