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

Example 16 with Alignment

use of dr.evolution.alignment.Alignment in project beast-mcmc by beast-dev.

the class BEAUTiImporter method importFastaFile.

// FASTA
private void importFastaFile(File file) throws IOException, ImportException {
    try {
        FileReader reader = new FileReader(file);
        FastaImporter importer = new FastaImporter(reader, Nucleotides.INSTANCE);
        Alignment alignment = importer.importAlignment();
        reader.close();
        setData(file.getName(), alignment, alignment, null, null, null, null);
    } catch (ImportException e) {
        throw new ImportException(e.getMessage());
    } catch (IOException e) {
        throw new IOException(e.getMessage());
    }
}

Example 17 with Alignment

use of dr.evolution.alignment.Alignment in project beast-mcmc by beast-dev.

the class NexusImporter method importAlignment.

// **************************************************************
// SequenceImporter IMPLEMENTATION
// **************************************************************
/**
     * importAlignment.
     */
public Alignment importAlignment() throws IOException, Importer.ImportException {
    boolean done = false;
    TaxonList taxonList = null;
    Alignment alignment = null;
    while (!done) {
        try {
            NexusImporter.NexusBlock block = findNextBlock();
            if (block == NexusImporter.TAXA_BLOCK) {
                taxonList = readTaxaBlock();
            } else if (block == NexusImporter.CALIBRATION_BLOCK) {
                if (taxonList == null) {
                    throw new MissingBlockException("TAXA block is missing");
                }
                readCalibrationBlock(taxonList);
            } else if (block == NexusImporter.CHARACTERS_BLOCK) {
                if (taxonList == null) {
                    throw new MissingBlockException("TAXA block is missing");
                }
                alignment = readCharactersBlock(taxonList);
                done = true;
            } 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 = readDataBlock();
                done = true;
            } else {
            // Ignore the block..
            }
        } catch (EOFException ex) {
            done = true;
        }
    }
    if (alignment == null) {
        throw new MissingBlockException("DATA or CHARACTERS block is missing");
    }
    return alignment;
}

Example 18 with Alignment

use of dr.evolution.alignment.Alignment 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 19 with Alignment

use of dr.evolution.alignment.Alignment in project beast-mcmc by beast-dev.

the class PatternListGenerator method writePatternList.

/**
     * Write a single pattern list
     *
     * @param partition the partition to write a pattern list for
     * @param offset    offset by
     * @param every     skip every
     * @param writer    the writer
     */
private void writePatternList(final PartitionData partition, int offset, int every, final String codonPrefix, final boolean unique, final boolean strip, final XMLWriter writer) {
    Alignment alignment = partition.getAlignment();
    int from = partition.getFromSite();
    int to = partition.getToSite();
    int partEvery = partition.getEvery();
    if (partEvery > 1 && every > 1)
        throw new IllegalArgumentException();
    if (from < 1)
        from = 1;
    every = Math.max(partEvery, every);
    from += offset;
    // this object is created solely to calculate the number of patterns in the alignment
    SitePatterns patterns = new SitePatterns(alignment, null, from - 1, to - 1, every, strip, unique);
    writer.writeComment("The " + (unique ? "unique " : "") + "patterns from " + from + " to " + (to > 0 ? to : "end") + ((every > 1) ? " every " + every : ""), "npatterns=" + patterns.getPatternCount());
    List<Attribute> attributes = new ArrayList<Attribute>();
    // no 11 of 112 codon, which uses mergePatterns id instead
    if (codonPrefix != null) {
        attributes.add(new Attribute.Default<String>(XMLParser.ID, partition.getPrefix() + codonPrefix + SitePatternsParser.PATTERNS));
    }
    attributes.add(new Attribute.Default<String>("from", "" + from));
    if (to >= 0)
        attributes.add(new Attribute.Default<String>("to", "" + to));
    if (every > 1) {
        attributes.add(new Attribute.Default<String>("every", "" + every));
    }
    if (!unique) {
        attributes.add(new Attribute.Default<Boolean>(SitePatternsParser.UNIQUE, false));
    }
    if (strip) {
        // default true
        attributes.add(new Attribute.Default<Boolean>(SitePatternsParser.STRIP, false));
    }
    // generate <patterns>
    writer.writeOpenTag(SitePatternsParser.PATTERNS, attributes);
    writer.writeIDref(AlignmentParser.ALIGNMENT, alignment.getId());
    writer.writeCloseTag(SitePatternsParser.PATTERNS);
}

Example 20 with Alignment

use of dr.evolution.alignment.Alignment in project beast-mcmc by beast-dev.

the class SubstitutionModelGenerator method writeBinaryCovarionModel.

/**
     * Write the Binary covarion model XML block
     *
     * @param writer the writer
     * @param model  the partition model to write
     */
public void writeBinaryCovarionModel(XMLWriter writer, PartitionSubstitutionModel model) {
    //        String dataTypeDescription = TwoStateCovarion.INSTANCE.getDescription(); // dataType="twoStateCovarion" for COVARION_MODEL
    String prefix = model.getPrefix();
    writer.writeComment("The Binary covarion model");
    writer.writeOpenTag(BinaryCovarionModelParser.COVARION_MODEL, new Attribute[] { new Attribute.Default<String>(XMLParser.ID, prefix + "bcov") });
    if (model.getFrequencyPolicy() == FrequencyPolicyType.EMPIRICAL) {
        List<AbstractPartitionData> partitions = options.getDataPartitions(model);
        Alignment alignment = ((PartitionData) partitions.get(0)).getAlignment();
        //            Patterns patterns = new Patterns(partitions.get(0).getAlignment());
        //            for (int i = 1; i < partitions.size(); i++) {
        //                patterns.addPatterns(partitions.get(i).getAlignment());
        //            }
        double[] frequencies = alignment.getStateFrequencies();
        writer.writeOpenTag(FrequencyModelParser.FREQUENCIES);
        writer.writeTag(ParameterParser.PARAMETER, new Attribute[] { new Attribute.Default<String>(XMLParser.ID, prefix + "frequencies"), new Attribute.Default<String>(ParameterParser.VALUE, frequencies[0] + " " + frequencies[1]) }, true);
        writer.writeCloseTag(FrequencyModelParser.FREQUENCIES);
    } else {
        writeFrequencyModelBinary(writer, model, prefix);
    }
    writeParameter(BinaryCovarionModelParser.HIDDEN_FREQUENCIES, prefix + "hfrequencies", 2, 0.5, 0.0, 1.0, // hfrequencies also 0.5 0.5
    writer);
    writeParameter(BinaryCovarionModelParser.ALPHA, "bcov.alpha", model, writer);
    writeParameter(BinaryCovarionModelParser.SWITCHING_RATE, "bcov.s", model, writer);
    writer.writeCloseTag(BinaryCovarionModelParser.COVARION_MODEL);
}