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

Example 66 with Tree

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

the class BEAUTiImporter method importNexusFile.

// nexus
private void importNexusFile(File file) throws IOException, ImportException {
    TaxonList taxa = null;
    SimpleAlignment alignment = null;
    List<Tree> trees = new ArrayList<Tree>();
    PartitionSubstitutionModel model = null;
    List<NexusApplicationImporter.CharSet> charSets = new ArrayList<NexusApplicationImporter.CharSet>();
    try {
        FileReader reader = new FileReader(file);
        NexusApplicationImporter importer = new NexusApplicationImporter(reader);
        boolean done = false;
        while (!done) {
            try {
                NexusBlock block = importer.findNextBlock();
                if (block == NexusImporter.TAXA_BLOCK) {
                    if (taxa != null) {
                        throw new MissingBlockException("TAXA block already defined");
                    }
                    taxa = importer.parseTaxaBlock();
                } else if (block == NexusImporter.CALIBRATION_BLOCK) {
                    if (taxa == null) {
                        throw new 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 MissingBlockException("TAXA block must be defined before a CHARACTERS block");
                    }
                    if (alignment != null) {
                        throw new MissingBlockException("CHARACTERS or DATA block already defined");
                    }
                    alignment = (SimpleAlignment) importer.parseCharactersBlock(taxa);
                } else if (block == NexusImporter.DATA_BLOCK) {
                    if (alignment != null) {
                        throw new 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 = (SimpleAlignment) importer.parseDataBlock(taxa);
                    if (taxa == null) {
                        taxa = alignment;
                    }
                } else if (block == NexusImporter.TREES_BLOCK) {
                    // I guess there is no reason not to allow multiple trees blocks
                    //                        if (trees.size() > 0) {
                    //                            throw new MissingBlockException("TREES block already defined");
                    //                        }
                    Tree[] treeArray = importer.parseTreesBlock(taxa);
                    trees.addAll(Arrays.asList(treeArray));
                    if (taxa == null && trees.size() > 0) {
                        taxa = trees.get(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 || block == NexusApplicationImporter.SETS_BLOCK) {
                    importer.parseAssumptionsBlock(charSets);
                } else {
                // Ignore the block..
                }
            } catch (EOFException ex) {
                done = true;
            }
        }
        reader.close();
        // 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 MissingBlockException("TAXON, DATA or CHARACTERS block is missing");
        }
    } catch (IOException e) {
        throw new IOException(e.getMessage());
    } catch (ImportException e) {
        throw new ImportException(e.getMessage());
    //        } catch (Exception e) {
    //            throw new Exception(e.getMessage());
    }
    setData(file.getName(), taxa, alignment, charSets, model, null, trees);
}

Example 67 with Tree

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

the class BEAUTiImporter method addTrees.

private void addTrees(List<Tree> trees) {
    if (trees != null && trees.size() > 0) {
        for (Tree tree : trees) {
            String id = tree.getId();
            if (id == null || id.trim().length() == 0) {
                tree.setId("tree_" + (options.userTrees.size() + 1));
            } else {
                String newId = id;
                int count = 1;
                for (Tree tree1 : options.userTrees) {
                    if (tree1.getId().equals(newId)) {
                        newId = id + "_" + count;
                        count++;
                    }
                }
                tree.setId(newId);
            }
            options.userTrees.add(tree);
        }
    }
}

Example 68 with Tree

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

the class MapperFrame method readFromFile.

protected boolean readFromFile(File file) throws IOException {
    Reader reader = new FileReader(file);
    BufferedReader bufferedReader = new BufferedReader(reader);
    String line = bufferedReader.readLine();
    while (line != null && line.length() == 0) {
        line = bufferedReader.readLine();
    }
    boolean isNexus = (line != null && line.toUpperCase().contains("#NEXUS"));
    reader = new FileReader(file);
    Tree tree = null;
    try {
    //            if (isNexus) {
    //                NexusImporter importer = new NexusImporter(reader);
    //                tree = importer.importTree(taxa);
    //            } else {
    //                NewickImporter importer = new NewickImporter(reader);
    //                tree = importer.importTree(taxa);
    //            }
    //        } catch (Importer.ImportException ime) {
    //            JOptionPane.showMessageDialog(this, "Error parsing imported file: " + ime,
    //                    "Error reading file",
    //                    JOptionPane.ERROR_MESSAGE);
    //            ime.printStackTrace();
    //            return false;
    //        } catch (IOException ioex) {
    //            JOptionPane.showMessageDialog(this, "File I/O Error: " + ioex,
    //                    "File I/O Error",
    //                    JOptionPane.ERROR_MESSAGE);
    //            ioex.printStackTrace();
    //            return false;
    } catch (Exception ex) {
        JOptionPane.showMessageDialog(this, "Fatal exception: " + ex, "Error reading file", JOptionPane.ERROR_MESSAGE);
        ex.printStackTrace();
        return false;
    }
    if (tree == null) {
        JOptionPane.showMessageDialog(this, "The file is not in a suitable format or contains no trees.", "Error reading file", JOptionPane.ERROR_MESSAGE);
        return false;
    }
    FlexibleTree binaryTree = new FlexibleTree(tree, true);
    binaryTree.resolveTree();
    trees.add(binaryTree);
    //        if (taxa == null) {
    //            taxa = binaryTree;
    //        }
    getExportDataAction().setEnabled(true);
    return true;
}

Example 69 with Tree

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

the class Coevolve method readTreeFile.

/**
     * @param fileName
     * @throws java.io.IOException
     */
private Tree readTreeFile(String fileName) throws java.io.IOException {
    Alignment alignment = null;
    Tree[] trees = null;
    TaxonList taxonList = null;
    try {
        FileReader reader = new FileReader(fileName);
        NexusImporter importer = new NexusImporter(reader);
        boolean done = false;
        while (!done) {
            try {
                NexusImporter.NexusBlock block = importer.findNextBlock();
                if (block == NexusImporter.TAXA_BLOCK) {
                    if (taxonList != null) {
                        throw new NexusImporter.MissingBlockException("TAXA block already defined");
                    }
                    taxonList = importer.parseTaxaBlock();
                } else if (block == NexusImporter.DATA_BLOCK) {
                    // A data block doesn't need a taxon block before it
                    // but if one exists then it will use it.
                    alignment = importer.parseDataBlock(taxonList);
                    if (taxonList == null) {
                        taxonList = alignment;
                    }
                } else if (block == NexusImporter.TREES_BLOCK) {
                    trees = importer.parseTreesBlock(taxonList);
                    if (taxonList == null) {
                        taxonList = alignment;
                    }
                } else {
                // Ignore the block..
                }
            } catch (EOFException ex) {
                done = true;
            }
        }
    } catch (Importer.ImportException ime) {
        System.err.println("Error reading alignment: " + ime);
    }
    return trees[0];
}

Example 70 with Tree

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

the class PathogenFrame method writeTreeFile.

protected void writeTreeFile(PrintStream ps, boolean newickFormat) throws IOException {
    Tree tree = pathogenPanel.getTreeAsViewed();
    //        if (newickFormat) {
    //            NewickExporter newickExporter = new NewickExporter(ps);
    //            newickExporter.exportTree(tree);
    //        } else {
    NexusExporter nexusExporter = new NexusExporter(new PrintStream(ps));
    nexusExporter.exportTree(tree);
//        }
}