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

Example 61 with Tree

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

the class NexusImporter method importNextTree.

/**
     * import the next tree.
     * return the tree or null if no more trees are available
     */
public Tree importNextTree() throws IOException, ImportException {
    // call hasTree to do the hard work...
    if (!hasTree()) {
        isReadingTreesBlock = false;
        return null;
    }
    Tree tree = nextTree;
    nextTree = null;
    return tree;
}

Example 62 with Tree

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

the class DataModelImporter method importNexusFile.

// nexus
private void importNexusFile(File file, DateGuesser guesser, Map dataModel) throws IOException, ImportException {
    TaxonList taxa = null;
    SimpleAlignment alignment = null;
    List<Tree> trees = new ArrayList<Tree>();
    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();
                    dataModel.put("taxa", createTaxonList(taxa));
                } 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.ASSUMPTIONS_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(dataModel, guesser, file.getName(), taxa, null, alignment, charSets, null, trees);
}

Example 63 with Tree

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

the class DataModelImporter method importFromTreeFile.

public Map importFromTreeFile(String fileName, Map dataModel) throws IOException, Importer.ImportException {
    Tree tree = null;
    try {
        Reader reader = new FileReader(fileName);
        BufferedReader bufferedReader = new BufferedReader(reader);
        String line = bufferedReader.readLine();
        while (line != null && line.length() == 0) {
            line = bufferedReader.readLine();
        }
        reader = new FileReader(fileName);
        if ((line != null && line.toUpperCase().contains("#NEXUS"))) {
            // is a NEXUS file
            NexusImporter importer = new NexusImporter(reader);
            tree = importer.importNextTree();
        } else {
            NewickImporter importer = new NewickImporter(reader);
            tree = importer.importNextTree();
        }
        bufferedReader.close();
    } catch (IOException e) {
        throw new IOException(e.getMessage());
    }
    if (tree != null) {
        dataModel.put("tree", TreeUtils.newick(tree));
    }
    return dataModel;
}

Example 64 with Tree

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

the class OldTreesPanel method setOptions.

public void setOptions(BeautiOptions options) {
    this.options = options;
    settingOptions = true;
    //        treePriorCombo.setSelectedItem(options.nodeHeightPrior);
    //
    //        groupCountField.setValue(options.skylineGroupCount);
    //        //samplingProportionField.setValue(options.birthDeathSamplingProportion);
    //
    //        parameterizationCombo.setSelectedIndex(options.parameterization);
    //        bayesianSkylineCombo.setSelectedIndex(options.skylineModel);
    //
    //        extendedBayesianSkylineCombo.setSelectedIndex(options.multiLoci ? 1 : 0);
    //
    //        gmrfBayesianSkyrideCombo.setSelectedIndex(options.skyrideSmoothing);
    //
    //        startingTreeCombo.setSelectedItem(options.startingTreeType);
    userTreeCombo.removeAllItems();
    if (options.userTrees.size() == 0) {
        userTreeCombo.addItem("no trees loaded");
        userTreeCombo.setEnabled(false);
    } else {
        for (Tree tree : options.userTrees) {
            userTreeCombo.addItem(tree.getId());
        }
        userTreeCombo.setEnabled(true);
    }
    setupPanel();
    settingOptions = false;
    validate();
    repaint();
}

Example 65 with Tree

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

the class PartitionTreeModelPanel method setUserSpecifiedStartingTree.

private void setUserSpecifiedStartingTree() {
    if (userTreeCombo.getSelectedItem() != null && (!userTreeCombo.getSelectedItem().toString().equalsIgnoreCase(NO_TREE))) {
        Tree seleTree = getSelectedUserTree();
        if (seleTree == null || isBifurcatingTree(seleTree, seleTree.getRoot())) {
            partitionTreeModel.setUserStartingTree(seleTree);
        } else {
            JOptionPane.showMessageDialog(parent, "The selected user-specified starting tree " + "is not fully bifurcating.\nBEAST requires rooted, bifurcating (binary) trees.", "Illegal user-specified starting tree", JOptionPane.ERROR_MESSAGE);
            userTreeCombo.setSelectedItem(NO_TREE);
            partitionTreeModel.setUserStartingTree(null);
        }
    }
}