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

Example 81 with Tree

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

the class BeautiTesterConfig method importFromFile.

public void importFromFile(String fileName, BeautiOptions options, boolean translate) {
    TaxonList taxa = null;
    Alignment alignment = null;
    Tree tree = null;
    PartitionSubstitutionModel model = null;
    java.util.List<NexusApplicationImporter.CharSet> charSets = new ArrayList<NexusApplicationImporter.CharSet>();
    try {
        FileReader reader = new FileReader(fileName);
        NexusApplicationImporter importer = new NexusApplicationImporter(reader);
        boolean done = false;
        while (!done) {
            try {
                NexusImporter.NexusBlock block = importer.findNextBlock();
                if (block == NexusImporter.TAXA_BLOCK) {
                    if (taxa != null) {
                        throw new NexusImporter.MissingBlockException("TAXA block already defined");
                    }
                    taxa = importer.parseTaxaBlock();
                } else if (block == NexusImporter.CALIBRATION_BLOCK) {
                    if (taxa == null) {
                        throw new NexusImporter.MissingBlockException("TAXA or DATA block must be defined before a CALIBRATION block");
                    }
                    importer.parseCalibrationBlock(taxa);
                } else if (block == NexusImporter.CHARACTERS_BLOCK) {
                    if (taxa == null) {
                        throw new NexusImporter.MissingBlockException("TAXA block must be defined before a CHARACTERS block");
                    }
                    if (alignment != null) {
                        throw new NexusImporter.MissingBlockException("CHARACTERS or DATA block already defined");
                    }
                    alignment = importer.parseCharactersBlock(options.taxonList);
                } else if (block == NexusImporter.DATA_BLOCK) {
                    if (alignment != null) {
                        throw new NexusImporter.MissingBlockException("CHARACTERS or DATA block already defined");
                    }
                    // A data block doesn't need a taxon block before it
                    // but if one exists then it will use it.
                    alignment = importer.parseDataBlock(options.taxonList);
                    if (taxa == null) {
                        taxa = alignment;
                    }
                } else if (block == NexusImporter.TREES_BLOCK) {
                    if (taxa == null) {
                        throw new NexusImporter.MissingBlockException("TAXA or DATA block must be defined before a TREES block");
                    }
                    if (tree != null) {
                        throw new NexusImporter.MissingBlockException("TREES block already defined");
                    }
                    Tree[] trees = importer.parseTreesBlock(taxa);
                    if (trees.length > 0) {
                        tree = trees[0];
                    }
                } else if (block == NexusApplicationImporter.PAUP_BLOCK) {
                    model = importer.parsePAUPBlock(options, charSets);
                } else if (block == NexusApplicationImporter.MRBAYES_BLOCK) {
                    model = importer.parseMrBayesBlock(options, charSets);
                } else if (block == NexusApplicationImporter.ASSUMPTIONS_BLOCK) {
                    importer.parseAssumptionsBlock(charSets);
                } else {
                // Ignore the block..
                }
            } catch (EOFException ex) {
                done = true;
            }
        }
        // Allow the user to load taxa only (perhaps from a tree file) so that they can sample from a prior...
        if (alignment == null && taxa == null) {
            throw new NexusImporter.MissingBlockException("TAXON, DATA or CHARACTERS block is missing");
        }
    } catch (FileNotFoundException fnfe) {
        System.err.println("File not found: " + fnfe);
        System.exit(1);
    } catch (Importer.ImportException ime) {
        System.err.println("Error parsing imported file: " + ime);
        System.exit(1);
    } catch (IOException ioex) {
        System.err.println("File I/O Error: " + ioex);
        System.exit(1);
    } catch (Exception ex) {
        System.err.println("Fatal exception: " + ex);
        System.exit(1);
    }
    if (options.taxonList == null) {
        // This is the first partition to be loaded...
        options.taxonList = new Taxa(taxa);
        // check the taxon names for invalid characters
        boolean foundAmp = false;
        for (int i = 0; i < taxa.getTaxonCount(); i++) {
            String name = taxa.getTaxon(i).getId();
            if (name.indexOf('&') >= 0) {
                foundAmp = true;
            }
        }
        if (foundAmp) {
            System.err.println("One or more taxon names include an illegal character ('&').");
            return;
        }
        // make sure they all have dates...
        for (int i = 0; i < taxa.getTaxonCount(); i++) {
            if (taxa.getTaxonAttribute(i, "date") == null) {
                java.util.Date origin = new java.util.Date(0);
                dr.evolution.util.Date date = dr.evolution.util.Date.createTimeSinceOrigin(0.0, Units.Type.YEARS, origin);
                taxa.getTaxon(i).setAttribute("date", date);
            }
        }
    } else {
        // This is an additional partition so check it uses the same taxa
        java.util.List<String> oldTaxa = new ArrayList<String>();
        for (int i = 0; i < options.taxonList.getTaxonCount(); i++) {
            oldTaxa.add(options.taxonList.getTaxon(i).getId());
        }
        java.util.List<String> newTaxa = new ArrayList<String>();
        for (int i = 0; i < taxa.getTaxonCount(); i++) {
            newTaxa.add(taxa.getTaxon(i).getId());
        }
        if (!(oldTaxa.containsAll(newTaxa) && oldTaxa.size() == newTaxa.size())) {
            System.err.println("This file contains different taxa from the previously loaded");
            return;
        }
    }
    String fileNameStem = dr.app.util.Utils.trimExtensions(fileName, new String[] { "NEX", "NEXUS", "TRE", "TREE" });
    if (alignment != null) {
        if (translate) {
            alignment = new ConvertAlignment(AminoAcids.INSTANCE, GeneticCode.UNIVERSAL, alignment);
        }
        java.util.List<PartitionData> partitions = new ArrayList<PartitionData>();
        if (charSets != null && charSets.size() > 0) {
            for (NexusApplicationImporter.CharSet charSet : charSets) {
                partitions.add(new PartitionData(options, charSet.getName(), fileName, new CharSetAlignment(charSet, alignment)));
            }
        } else {
            partitions.add(new PartitionData(options, fileNameStem, fileName, alignment));
        }
        for (PartitionData partition : partitions) {
            if (model != null) {
                partition.setPartitionSubstitutionModel(model);
            //                    options.addPartitionSubstitutionModel(model);
            } else {
                for (PartitionSubstitutionModel pm : options.getPartitionSubstitutionModels()) {
                    if (pm.getDataType() == alignment.getDataType()) {
                        partition.setPartitionSubstitutionModel(pm);
                    }
                }
                if (partition.getPartitionSubstitutionModel() == null) {
                    PartitionSubstitutionModel pm = new PartitionSubstitutionModel(options, partition);
                    partition.setPartitionSubstitutionModel(pm);
                //                        options.addPartitionSubstitutionModel(pm);
                }
            }
            options.dataPartitions.add(partition);
        }
    }
    calculateHeights(options);
}

Example 82 with Tree

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

the class NexusImporter method readNextTree.

private Tree readNextTree(HashMap<String, Taxon> translationList, String[] lastToken, TaxonList taxonList) throws ImportException, IOException {
    try {
        Tree tree = null;
        String token = lastToken[0];
        if (token.equalsIgnoreCase("UTREE") || token.equalsIgnoreCase("TREE")) {
            if (nextCharacter() == '*') {
                // Star is used to specify a default tree - ignore it
                readCharacter();
            }
            String token2 = readToken("=;");
            // Save tree comment and attach it later
            final String comment = getLastMetaComment();
            clearLastMetaComment();
            if (getLastDelimiter() != '=') {
                throw new BadFormatException("Missing label for tree'" + token2 + "' or missing '=' in TREE command of TREES block");
            }
            try {
                if (nextCharacter() != '(') {
                    throw new BadFormatException("Missing tree definition in TREE command of TREES block");
                }
                // tree special comments
                final String scomment = getLastMetaComment();
                clearLastMetaComment();
                FlexibleNode root = readInternalNode(translationList);
                if (translationList != null) {
                    // this ensures that if a translation list is used, the external node numbers
                    // of the trees correspond as well.
                    Map<Taxon, Integer> taxonNumberMap = new HashMap<Taxon, Integer>();
                    int count = 0;
                    for (String label : translationList.keySet()) {
                        Taxon taxon = translationList.get(label);
                        int number;
                        if (taxonList != null) {
                            // Map back to original numbering from TaxonList
                            number = taxonList.getTaxonIndex(taxon);
                        } else {
                            // Old functionality
                            try {
                                number = Integer.parseInt(label) - 1;
                            } catch (NumberFormatException nfe) {
                                number = count;
                            }
                        }
                        taxonNumberMap.put(taxon, number);
                        count++;
                    }
                    tree = new FlexibleTree(root, false, true, taxonNumberMap);
                } else {
                    tree = new FlexibleTree(root, false, true, null);
                }
                tree.setId(token2);
                if (getLastDelimiter() == ':') {
                    // in case the root has a branch length, skip it
                    readToken(";");
                    if (getLastMetaComment() != null) {
                        // \[&label[=value][,label[=value]>[,/..]]\]
                        try {
                            parseMetaCommentPairs(getLastMetaComment(), root);
                        } catch (BadFormatException bfe) {
                        // ignore it
                        }
                        clearLastMetaComment();
                    }
                }
                if (getLastDelimiter() != ';') {
                    throw new BadFormatException("Expecting ';' after tree, '" + token2 + "', TREE command of TREES block");
                }
                if (scomment != null) {
                    // below is correct only if [&W] appears on it own
                    String c = scomment;
                    while (c.length() > 0) {
                        final char ch = c.charAt(0);
                        if (ch == ';') {
                            c = c.substring(1);
                            continue;
                        }
                        if (ch == 'R') {
                            // we only have rooted trees anyway
                            c = c.substring(1);
                        } else if (ch == 'W') {
                            int e = c.indexOf(';');
                            if (e < 0)
                                e = c.length();
                            try {
                                final Float value = new Float(c.substring(2, e));
                                tree.setAttribute("weight", value);
                            } catch (NumberFormatException ex) {
                            // don't fail, ignore
                            }
                            c = c.substring(e);
                        } else {
                            c = c.substring(1);
                        }
                    }
                }
                if (comment != null) {
                    try {
                        parseMetaCommentPairs(comment, tree);
                    } catch (Importer.BadFormatException e) {
                        // set generic comment attribute
                        tree.setAttribute("comment", comment);
                    }
                }
            } catch (EOFException e) {
                // If we reach EOF we may as well return what we have?
                return tree;
            }
            token = readToken(";");
        } else if (token.equalsIgnoreCase("ENDBLOCK") || token.equalsIgnoreCase("END")) {
            return null;
        } else {
            throw new BadFormatException("Unknown command '" + token + "' in TREES block");
        }
        //added this to escape readNextTree loop correctly -- AJD
        lastToken[0] = token;
        return tree;
    } catch (EOFException e) {
        return null;
    }
}

Example 83 with Tree

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

the class NexusImporter method readTreesBlock.

/**
     * Reads a 'TREES' block.
     */
private Tree[] readTreesBlock(TaxonList taxonList, boolean useTaxonListNumbering) throws ImportException, IOException {
    ArrayList<Tree> trees = new ArrayList<Tree>();
    String[] lastToken = new String[1];
    HashMap<String, Taxon> translationList = readTranslationList(taxonList, lastToken);
    boolean done = false;
    do {
        Tree tree = readNextTree(translationList, lastToken, useTaxonListNumbering ? taxonList : null);
        if (tree != null) {
            trees.add(tree);
        } else {
            done = true;
        }
    } while (!done);
    if (trees.size() == 0) {
        throw new BadFormatException("No trees defined in TREES block");
    }
    Tree[] treeArray = new Tree[trees.size()];
    trees.toArray(treeArray);
    nextBlock = UNKNOWN_BLOCK;
    return treeArray;
}

Example 84 with Tree

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

the class MigrateTreeImporter method importTrees.

public Tree[] importTrees(TaxonList taxonList) throws IOException, ImportException {
    Tree[] trees = super.importTrees(taxonList);
    for (Tree tree : trees) {
        // convert toPops to pops
        for (int i = 0; i < tree.getNodeCount(); i++) {
            NodeRef node = tree.getNode(i);
            Object toPop = tree.getNodeAttribute(node, TO_POP);
            Object pop = tree.getNodeAttribute(node, POP);
            if (toPop != null && pop != null && !toPop.equals(pop)) {
                String nodeName = node.getNumber() + "";
                if (tree.isExternal(node)) {
                    nodeName = tree.getTaxonId(node.getNumber());
                }
                if (tree.isRoot(node))
                    nodeName = "root";
                throw new RuntimeException(TO_POP + " = " + toPop + ", " + POP + " = " + pop + " in node " + nodeName);
            }
            if (pop == null && toPop != null) {
                ((MutableTree) tree).setNodeAttribute(node, POP, toPop);
            }
        }
        // convert fromPops to pops
        for (int i = 0; i < tree.getNodeCount(); i++) {
            NodeRef node = tree.getNode(i);
            if (!tree.isRoot(node)) {
                NodeRef parent = tree.getParent(node);
                Object fromPop = tree.getNodeAttribute(node, FROM_POP);
                Object pop = tree.getNodeAttribute(parent, POP);
                if (fromPop != null && pop != null && !fromPop.equals(pop)) {
                    throw new RuntimeException(FROM_POP + " = " + fromPop + ", " + POP + " = " + pop);
                }
                if (pop == null && fromPop != null) {
                    ((MutableTree) tree).setNodeAttribute(parent, POP, fromPop);
                }
            }
        }
        // fill gaps with parent pops
        fillInternalGaps(tree, tree.getRoot());
        fillExternalGaps(tree);
    }
    return trees;
}

Example 85 with Tree

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

the class NexusImporter method main.

public static void main(String[] args) throws IOException, ImportException {
    if (args.length > 3) {
        int sampleFrequency = Integer.parseInt(args[1]);
        boolean includeBranchLengths = Boolean.getBoolean(args[2]);
        boolean isNexus = Boolean.getBoolean(args[3]);
        NexusImporter nexusImporter = null;
        BufferedReader reader = null;
        if (isNexus) {
            nexusImporter = new NexusImporter(new FileReader(args[0]));
        } else {
            reader = new BufferedReader(new FileReader(args[0]));
        }
        int index = 0;
        int count = 0;
        String line = null;
        if (!isNexus)
            line = reader.readLine();
        while (line != null || (isNexus && nexusImporter.hasTree())) {
            Tree tree;
            if (isNexus) {
                tree = nexusImporter.importNextTree();
            } else {
                String treeString = line.substring(line.indexOf('(')).trim();
                java.io.Reader stringReader = new java.io.StringReader(treeString);
                NewickImporter importer = new NewickImporter(stringReader);
                tree = importer.importNextTree();
            }
            if (index % sampleFrequency == 0) {
                if (includeBranchLengths) {
                    System.out.println(TreeUtils.newick(tree));
                } else {
                    System.out.println(TreeUtils.newickNoLengths(tree));
                    count += 1;
                }
            }
            index += 1;
            if (!isNexus)
                line = reader.readLine();
        }
        System.out.println(count + " trees");
    } else {
        System.err.println("usage: filterTrees <tree-file-name> <sample-frequency> <include-branch-lengths>");
    }
}