Examples with CharSetAlignment dr.evolution.alignment.CharSetAlignment used on opensource projects

Example 1 with CharSetAlignment

use of dr.evolution.alignment.CharSetAlignment 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);
}