Examples with TaxonList dr.evolution.util.TaxonList used on opensource projects

Example 26 with TaxonList

use of dr.evolution.util.TaxonList in project beast-mcmc by beast-dev.

the class FixedDriftModelParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    /*
        String idOne = xo.getStringAttribute(RATE_ONE_ID);

        String idTwo = xo.getStringAttribute(RATE_TWO_ID);

        Parameter rateOne = (Parameter) xo.getElementFirstChild(RATE_ONE);

        Parameter rateTwo = (Parameter) xo.getElementFirstChild(RATE_TWO);

        Parameter remainingRates = (Parameter) xo.getElementFirstChild(REMAINING_RATES);
        */
    TaxonList taxonList = (TaxonList) xo.getElementFirstChild(BACKBONE_TAXON_LIST);
    TreeModel treeModel = (TreeModel) xo.getChild(TreeModel.class);
    Parameter backboneDrift = (Parameter) xo.getElementFirstChild(BACKBONE_DRIFT);
    Parameter otherDrift = (Parameter) xo.getElementFirstChild(OTHER_DRIFT);
    Logger.getLogger("dr.evomodel").info("Using fixed drift model.");
    return new FixedDriftModel(treeModel, backboneDrift, otherDrift, taxonList);
//  return new FixedDriftModel(rateOne, rateTwo, remainingRates, idOne, idTwo);
}

Example 27 with TaxonList

use of dr.evolution.util.TaxonList 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 28 with TaxonList

use of dr.evolution.util.TaxonList 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 29 with TaxonList

use of dr.evolution.util.TaxonList in project beast-mcmc by beast-dev.

the class BEAUTiImporter method importBEASTFile.

// xml
private void importBEASTFile(File file) throws IOException, ImportException, JDOMException {
    try {
        FileReader reader = new FileReader(file);
        BeastImporter importer = new BeastImporter(reader);
        List<TaxonList> taxonLists = new ArrayList<TaxonList>();
        List<Alignment> alignments = new ArrayList<Alignment>();
        importer.importBEAST(taxonLists, alignments);
        TaxonList taxa = taxonLists.get(0);
        int count = 1;
        for (Alignment alignment : alignments) {
            String name = file.getName();
            if (alignment.getId() != null && alignment.getId().length() > 0) {
                name = alignment.getId();
            } else {
                if (alignments.size() > 1) {
                    name += count;
                }
            }
            setData(name, taxa, alignment, null, null, null, null);
            count++;
        }
        // assume that any additional taxon lists are taxon sets...
        for (int i = 1; i < taxonLists.size(); i++) {
            Taxa taxonSet = (Taxa) taxonLists.get(i);
            options.taxonSets.add(taxonSet);
            options.taxonSetsMono.put(taxonSet, false);
            options.taxonSetsIncludeStem.put(taxonSet, false);
            options.taxonSetsTreeModel.put(taxonSet, options.getPartitionTreeModels().get(0));
        }
        reader.close();
    } catch (JDOMException e) {
        throw new JDOMException(e.getMessage());
    } catch (ImportException e) {
        throw new ImportException(e.getMessage());
    } catch (IOException e) {
        throw new IOException(e.getMessage());
    }
}

Example 30 with TaxonList

use of dr.evolution.util.TaxonList 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];
}