Examples with Tree dr.evolution.tree.Tree used on opensource projects

Example 96 with Tree

use of dr.evolution.tree.Tree in project beast-mcmc by beast-dev.

the class GaussianProcessMultilocusSkytrackLikelihood method makeTreeIntervalList.

//                  OK
private void makeTreeIntervalList(List<Tree> treeList, boolean add) {
    if (intervalsList == null) {
        intervalsList = new ArrayList<TreeIntervals>();
    } else {
        intervalsList.clear();
    }
    for (Tree tree : treeList) {
        numIntervals += tree.getExternalNodeCount();
        intervalsList.add(new TreeIntervals(tree));
        if (add && tree instanceof TreeModel) {
            addModel((TreeModel) tree);
        }
    }
}

Example 97 with Tree

use of dr.evolution.tree.Tree in project beast-mcmc by beast-dev.

the class GMRFFixedGridLikelihood method run.

public static void run() throws Exception {
    NewickImporter importer = new NewickImporter("((((5:0.5,1:0.2):0.5,0:1):0.2,2:0.8):0.2,3:1.4)");
    Tree tree = importer.importNextTree();
    double[] data = new double[15];
    double[] times = new double[15];
    data[0] = 1.0;
    times[0] = 0.05;
    for (int i = 1; i < data.length; i++) {
        data[i] = data[i - 1] + 0.5;
        times[i] = times[i - 1] + 0.1;
    }
    GMRFFixedGridLikelihood like = new GMRFFixedGridLikelihood(tree, new Parameter.Default(data), new Parameter.Default(times), 4);
    System.out.println(like.getLogLikelihood());
}

Example 98 with Tree

use of dr.evolution.tree.Tree in project beast-mcmc by beast-dev.

the class CodonPartitionedRobustCounting method setupTraits.

private void setupTraits() {
    TreeTrait baseTrait = new TreeTrait.DA() {

        public String getTraitName() {
            return BASE_TRAIT_PREFIX + codonLabeling.getText();
        }

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

        public double[] getTrait(Tree tree, NodeRef node) {
            return getExpectedCountsForBranch(node);
        }

        public boolean getLoggable() {
            return false;
        }
    };
    if (saveCompleteHistory) {
        TreeTrait stringTrait = new TreeTrait.SA() {

            public String getTraitName() {
                return COMPLETE_HISTORY_PREFIX + codonLabeling.getText();
            }

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

            public boolean getFormatAsArray() {
                return true;
            }

            public String[] getTrait(Tree tree, NodeRef node) {
                // Lazy simulation of complete histories
                double[] count = getExpectedCountsForBranch(node);
                List<String> events = new ArrayList<String>();
                for (int i = 0; i < numCodons; i++) {
                    String eventString = completeHistoryPerNode[node.getNumber()][i];
                    if (eventString != null) {
                        if (eventString.contains("},{")) {
                            // There are multiple events
                            String[] elements = eventString.split("(?<=\\}),(?=\\{)");
                            for (String e : elements) {
                                events.add(e);
                            }
                        } else {
                            events.add(eventString);
                        }
                    }
                }
                if (DEBUG) {
                    double sum = 0.0;
                    for (double d : count) {
                        if (d > 0.0) {
                            sum += 1;
                        }
                    }
                    System.err.println(events.size() + " " + sum);
                    if (Math.abs(events.size() - sum) > 0.5) {
                        System.err.println("Error");
                        for (int i = 0; i < count.length; ++i) {
                            if (count[i] != 0.0) {
                                System.err.println(i + ": " + count[i] + completeHistoryPerNode[node.getNumber()][i]);
                            }
                        }
                        System.err.println("Error");
                        int c = 0;
                        for (String s : events) {
                            c++;
                            System.err.println(c + ":" + s);
                        }
                        System.exit(-1);
                    }
                }
                String[] array = new String[events.size()];
                events.toArray(array);
                return array;
            }

            public boolean getLoggable() {
                return true;
            }
        };
        treeTraits.addTrait(stringTrait);
    }
    TreeTrait unconditionedSum;
    if (!TRIAL) {
        unconditionedSum = new TreeTrait.D() {

            public String getTraitName() {
                return UNCONDITIONED_PREFIX + codonLabeling.getText();
            }

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

            public Double getTrait(Tree tree, NodeRef node) {
                return getUnconditionedTraitValue();
            }

            public boolean getLoggable() {
                return false;
            }
        };
    } else {
        unconditionedSum = new TreeTrait.DA() {

            public String getTraitName() {
                return UNCONDITIONED_PREFIX + codonLabeling.getText();
            }

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

            public double[] getTrait(Tree tree, NodeRef node) {
                return getUnconditionedTraitValues();
            }

            public boolean getLoggable() {
                return false;
            }
        };
    }
    TreeTrait sumOverTreeTrait = new TreeTrait.SumOverTreeDA(SITE_SPECIFIC_PREFIX + codonLabeling.getText(), baseTrait, includeExternalBranches, includeInternalBranches) {

        @Override
        public boolean getLoggable() {
            return false;
        }
    };
    // This should be the default output in tree logs
    TreeTrait sumOverSitesTrait = new TreeTrait.SumAcrossArrayD(codonLabeling.getText(), baseTrait) {

        @Override
        public boolean getLoggable() {
            return true;
        }
    };
    // This should be the default output in columns logs
    String name = prefix != null ? prefix + TOTAL_PREFIX + codonLabeling.getText() : TOTAL_PREFIX + codonLabeling.getText();
    TreeTrait sumOverSitesAndTreeTrait = new TreeTrait.SumOverTreeD(name, sumOverSitesTrait, includeExternalBranches, includeInternalBranches) {

        @Override
        public boolean getLoggable() {
            return true;
        }
    };
    treeTraitLogger = new TreeTraitLogger(tree, new TreeTrait[] { sumOverSitesAndTreeTrait });
    treeTraits.addTrait(baseTrait);
    treeTraits.addTrait(unconditionedSum);
    treeTraits.addTrait(sumOverSitesTrait);
    treeTraits.addTrait(sumOverTreeTrait);
    treeTraits.addTrait(sumOverSitesAndTreeTrait);
    if (doUnconditionedPerBranch) {
        TreeTrait unconditionedBase = new TreeTrait.DA() {

            public String getTraitName() {
                return UNCONDITIONED_PER_BRANCH_PREFIX + codonLabeling.getText();
            }

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

            public double[] getTrait(Tree tree, NodeRef node) {
                return getUnconditionalCountsForBranch(node);
            }

            public boolean getLoggable() {
                // TODO Should be switched to true to log unconditioned values per branch
                return false;
            }
        };
        TreeTrait sumUnconditionedOverSitesTrait = new TreeTrait.SumAcrossArrayD(UNCONDITIONED_PER_BRANCH_PREFIX + codonLabeling.getText(), unconditionedBase) {

            @Override
            public boolean getLoggable() {
                return true;
            }
        };
        String nameU = prefix != null ? prefix + UNCONDITIONED_TOTAL_PREFIX + codonLabeling.getText() : UNCONDITIONED_TOTAL_PREFIX + codonLabeling.getText();
        TreeTrait sumUnconditionedOverSitesAndTreeTrait = new TreeTrait.SumOverTreeD(nameU, sumUnconditionedOverSitesTrait, includeExternalBranches, includeInternalBranches) {

            public boolean getLoggable() {
                return true;
            }
        };
        treeTraitLogger = new TreeTraitLogger(tree, new TreeTrait[] { sumOverSitesAndTreeTrait, sumUnconditionedOverSitesAndTreeTrait });
        treeTraits.addTrait(unconditionedBase);
        treeTraits.addTrait(sumUnconditionedOverSitesTrait);
    }
}

Example 99 with Tree

use of dr.evolution.tree.Tree in project beast-mcmc by beast-dev.

the class ConditionalCladeFrequency method report.

/**
     * Creates the report. The estimated posterior of the given tree is printed.
     *
     * @throws IOException if general I/O error occurs
     */
public void report(Reader r) throws IOException, Importer.ImportException {
    System.err.println("making report");
    ArrayList<Tree> referenceTrees = new ArrayList<Tree>();
    BufferedReader reader = new BufferedReader(r);
    String line = reader.readLine();
    if (line.toUpperCase().startsWith("#NEXUS")) {
        NexusImporter importer = new NexusImporter(reader);
        Tree[] trees = importer.importTrees(null);
        for (Tree tree : trees) {
            referenceTrees.add(tree);
            SimpleTree sTree = new SimpleTree(tree);
            System.out.println("Estimated marginal posterior by condiational clade frequencies:");
            System.out.println(getTreeProbability(sTree) + "\t\t" + sTree);
        }
    } else {
        throw new RuntimeException("Could not read reference tree. Only Nexus format is supported.");
    }
    System.out.flush();
}

Example 100 with Tree

use of dr.evolution.tree.Tree in project beast-mcmc by beast-dev.

the class ConditionalCladeFrequency method analyzeTrace.

/**
     * Actually analyzes the trace given the burn-in. Each tree from the trace
     * is read and the conditional clade frequencies incremented.
     *
     * @param verbose if true then progress is logged to stdout
     */
public void analyzeTrace(boolean verbose) {
    if (verbose) {
        if (traces.length > 1)
            System.out.println("Combining " + traces.length + " traces.");
    }
    // get first tree to extract the taxon
    Tree tree = getTree(0);
    // read every tree from the trace
    for (TreeTrace trace : traces) {
        // do some output stuff
        int treeCount = trace.getTreeCount(burnin * trace.getStepSize());
        double stepSize = treeCount / 60.0;
        int counter = 1;
        if (verbose) {
            System.out.println("Analyzing " + treeCount + " trees...");
            System.out.println("0              25             50             75            100");
            System.out.println("|--------------|--------------|--------------|--------------|");
            System.out.print("*");
        }
        for (int i = 1; i < treeCount; i++) {
            // get the next tree
            tree = trace.getTree(i, burnin * trace.getStepSize());
            // add the tree and its clades to the frequencies
            addTree(tree);
            // some more output stuff
            if (i >= (int) Math.round(counter * stepSize) && counter <= 60) {
                if (verbose) {
                    System.out.print("*");
                    System.out.flush();
                }
                counter += 1;
            }
        }
        if (verbose) {
            System.out.println("*");
        }
    }
}