Examples with FilteredAlignment beast.evolution.alignment.FilteredAlignment used on opensource projects

Example 16 with FilteredAlignment

use of beast.evolution.alignment.FilteredAlignment in project beast2 by CompEvol.

the class ThreadedTreeLikelihood method initAndValidate.

@Override
public void initAndValidate() {
    threadCount = BeastMCMC.m_nThreads;
    if (maxNrOfThreadsInput.get() > 0) {
        threadCount = Math.min(maxNrOfThreadsInput.get(), BeastMCMC.m_nThreads);
    }
    String instanceCount = System.getProperty("beast.instance.count");
    if (instanceCount != null && instanceCount.length() > 0) {
        threadCount = Integer.parseInt(instanceCount);
    }
    logPByThread = new double[threadCount];
    // sanity check: alignment should have same #taxa as tree
    if (dataInput.get().getTaxonCount() != treeInput.get().getLeafNodeCount()) {
        throw new IllegalArgumentException("The number of nodes in the tree does not match the number of sequences");
    }
    treelikelihood = new TreeLikelihood[threadCount];
    if (dataInput.get().isAscertained) {
        Log.warning.println("Note, can only use single thread per alignment because the alignment is ascertained");
        threadCount = 1;
    }
    if (threadCount <= 1) {
        treelikelihood[0] = new TreeLikelihood();
        treelikelihood[0].setID(getID() + "0");
        treelikelihood[0].initByName("data", dataInput.get(), "tree", treeInput.get(), "siteModel", siteModelInput.get(), "branchRateModel", branchRateModelInput.get(), "useAmbiguities", useAmbiguitiesInput.get(), "scaling", scalingInput.get() + "");
        treelikelihood[0].getOutputs().add(this);
        likelihoodsInput.get().add(treelikelihood[0]);
    } else {
        pool = Executors.newFixedThreadPool(threadCount);
        calcPatternPoints(dataInput.get().getSiteCount());
        for (int i = 0; i < threadCount; i++) {
            Alignment data = dataInput.get();
            String filterSpec = (patternPoints[i] + 1) + "-" + (patternPoints[i + 1]);
            if (data.isAscertained) {
                filterSpec += data.excludefromInput.get() + "-" + data.excludetoInput.get() + "," + filterSpec;
            }
            treelikelihood[i] = new TreeLikelihood();
            treelikelihood[i].setID(getID() + i);
            treelikelihood[i].getOutputs().add(this);
            likelihoodsInput.get().add(treelikelihood[i]);
            FilteredAlignment filter = new FilteredAlignment();
            if (i == 0 && dataInput.get() instanceof FilteredAlignment && ((FilteredAlignment) dataInput.get()).constantSiteWeightsInput.get() != null) {
                filter.initByName("data", dataInput.get(), /*, "userDataType", m_data.get().getDataType()*/
                "filter", filterSpec, "constantSiteWeights", ((FilteredAlignment) dataInput.get()).constantSiteWeightsInput.get());
            } else {
                filter.initByName("data", dataInput.get(), /*, "userDataType", m_data.get().getDataType()*/
                "filter", filterSpec);
            }
            treelikelihood[i].initByName("data", filter, "tree", treeInput.get(), "siteModel", duplicate((BEASTInterface) siteModelInput.get(), i), "branchRateModel", duplicate(branchRateModelInput.get(), i), "useAmbiguities", useAmbiguitiesInput.get(), "scaling", scalingInput.get() + "");
            likelihoodCallers.add(new TreeLikelihoodCaller(treelikelihood[i], i));
        }
    }
}

Example 17 with FilteredAlignment

use of beast.evolution.alignment.FilteredAlignment in project Babel by rbouckaert.

the class NexusParser method parseAssumptionsBlock.

// parseDataBlock
/**
 * parse assumptions block
 * begin assumptions;
 * charset firsthalf = 1-449;
 * charset secondhalf = 450-898;
 * charset third = 1-457\3 662-896\3;
 * end;
 *
 * begin assumptions;
 * wtset MySoapWeights (VECTOR) = 13 13 13 50 50 88 8
 * end;
 */
void parseAssumptionsBlock(final BufferedReader fin) throws Exception {
    if (true) {
        return;
    }
    String str;
    do {
        str = nextLine(fin);
        if (str.toLowerCase().matches("\\s*charset\\s.*")) {
            // remove text in brackets (as TreeBase files are wont to contain)
            str = str.replaceAll("\\(.*\\)", "");
            // clean up spaces
            str = str.replaceAll("^\\s+", "");
            str = str.replaceAll("\\s*-\\s*", "-");
            str = str.replaceAll("\\s*\\\\\\s*", "\\\\");
            str = str.replaceAll("\\s*;", "");
            final String[] strs = str.trim().split("\\s+");
            final String id = strs[1];
            String rangeString = "";
            for (int i = 3; i < strs.length; i++) {
                rangeString += strs[i] + " ";
            }
            rangeString = rangeString.trim().replace(' ', ',');
            final FilteredAlignment alignment = new FilteredAlignment();
            alignment.setID(id);
            alignment.alignmentInput.setValue(m_alignment, alignment);
            alignment.filterInput.setValue(rangeString, alignment);
            alignment.initAndValidate();
            filteredAlignments.add(alignment);
        } else if (str.toLowerCase().matches("\\s*wtset\\s.*")) {
            String[] strs = str.split("=");
            if (strs.length > 1) {
                str = strs[strs.length - 1].trim();
                strs = str.split("\\s+");
                int[] weights = new int[strs.length];
                for (int i = 0; i < strs.length; i++) {
                    weights[i] = Integer.parseInt(strs[i]);
                }
                if (m_alignment != null) {
                    if (weights.length != m_alignment.getSiteCount()) {
                        throw new RuntimeException("Number of weights (" + weights.length + ") " + "does not match number of sites in alignment(" + m_alignment.getSiteCount() + ")");
                    }
                    StringBuilder weightStr = new StringBuilder();
                    for (String str2 : strs) {
                        weightStr.append(str2);
                        weightStr.append(',');
                    }
                    weightStr.delete(weightStr.length() - 1, weightStr.length());
                    m_alignment.siteWeightsInput.setValue(weightStr.toString(), m_alignment);
                    m_alignment.initAndValidate();
                } else {
                    Log.warning.println("WTSET was specified before alignment. WTSET is ignored.");
                }
            }
        } else if (str.toLowerCase().matches("^\\s*taxset\\s.*")) {
            // define taxon set, e.g.
            // begin set;
            // taxset germanic = english german dutch;
            // taxset romance = italian spanish rumenian;
            // end;
            String[] strs = str.split("=");
            if (strs.length > 1) {
                String str0 = strs[0].trim();
                String[] strs2 = str0.split("\\s+");
                if (strs2.length != 2) {
                    throw new RuntimeException("expected 'taxset <name> = ...;' but did not get two words before the = sign: " + str);
                }
                String taxonSetName = strs2[1];
                str0 = strs[strs.length - 1].trim();
                if (!str0.endsWith(";")) {
                    throw new RuntimeException("expected 'taxset <name> = ...;' semi-colin is missing: " + str);
                }
                str0 = str0.replaceAll(";", "");
                String[] taxonNames = str0.split("\\s+");
                TaxonSet taxonset = new TaxonSet();
                for (String taxon : taxonNames) {
                    taxonset.taxonsetInput.get().add(new Taxon(taxon));
                }
                taxonset.setID(taxonSetName);
                taxonsets.add(taxonset);
            }
        } else if (str.toLowerCase().matches("^\\s*calibrate\\s.*")) {
            // define calibration represented by an MRCAPRior,
            // taxon sets need to be specified earlier, but can also be a single taxon
            // e.g.
            // begin mrbayes;
            // calibrate germanic = normal(1000,50)
            // calibrate hittite = normal(3450,100)
            // calibrate english = fixed(0)
            // end;
            String[] strs = str.split("=");
            if (strs.length > 1) {
                String str0 = strs[0].trim();
                String[] strs2 = str0.split("\\s+");
                if (strs2.length != 2) {
                    throw new RuntimeException("expected 'calibrate <name> = ...' but did not get two words before the = sign: " + str);
                }
                // first, get the taxon
                String taxonSetName = strs2[1].replaceAll("'\"", "");
                Taxon taxonset = null;
                for (Taxon t : taxonsets) {
                    if (t.getID().equals(taxonSetName)) {
                        taxonset = t;
                    }
                }
                if (taxonset == null) {
                    for (String t : taxa) {
                        if (t.equals(taxonSetName)) {
                            taxonset = new Taxon(t);
                        }
                    }
                }
                if (taxonset == null) {
                    throw new RuntimeException("Could not find taxon/taxonset " + taxonSetName + " in calibration: " + str);
                }
                // next get the calibration
                str0 = strs[strs.length - 1].trim();
                String[] strs3 = str0.split("[\\(,\\)]");
                ParametricDistribution distr = null;
                switch(strs3[0]) {
                    case "normal":
                        distr = new Normal();
                        distr.initByName("mean", strs3[1], "sigma", strs3[2]);
                        distr.setID("Normal.0");
                        break;
                    case "uniform":
                        distr = new Uniform();
                        distr.initByName("lower", strs3[1], "upper", strs3[2]);
                        distr.setID("Uniform.0");
                        break;
                    case "fixed":
                        // uniform with lower == upper
                        distr = new Uniform();
                        distr.initByName("lower", strs3[1], "upper", strs3[1]);
                        distr.setID("Uniform.0");
                        break;
                    case "offsetlognormal":
                        distr = new LogNormalDistributionModel();
                        distr.initByName("offset", strs3[1], "M", strs3[2], "S", strs3[3], "meanInRealSpace", true);
                        distr.setID("LogNormal.0");
                        break;
                    case "lognormal":
                        distr = new LogNormalDistributionModel();
                        distr.initByName("M", strs3[1], "S", strs3[2], "meanInRealSpace", true);
                        distr.setID("LogNormal.0");
                        break;
                    case "offsetexponential":
                        distr = new Exponential();
                        distr.initByName("offset", strs3[1], "mean", strs3[2]);
                        distr.setID("Exponential.0");
                        break;
                    case "gamma":
                        distr = new Gamma();
                        distr.initByName("alpha", strs3[1], "beta", strs3[2]);
                        distr.setID("Gamma.0");
                        break;
                    case "offsetgamma":
                        distr = new Gamma();
                        distr.initByName("offset", strs3[1], "alpha", strs3[2], "beta", strs3[3]);
                        distr.setID("Gamma.0");
                        break;
                    default:
                        throw new RuntimeException("Unknwon distribution " + strs3[0] + "in calibration: " + str);
                }
                MRCAPrior prior = new MRCAPrior();
                prior.isMonophyleticInput.setValue(true, prior);
                prior.distInput.setValue(distr, prior);
                prior.taxonsetInput.setValue(taxonset, prior);
                prior.setID(taxonset.getID() + ".prior");
                // should set Tree before initialising, but we do not know the tree yet...
                calibrations.add(prior);
            }
        }
    } while (!str.toLowerCase().contains("end;"));
}

Example 18 with FilteredAlignment

use of beast.evolution.alignment.FilteredAlignment in project feast by tgvaughan.

the class SequenceExtractor method main.

public static void main(String[] args) {
    if (args.length < 2) {
        System.out.println("Usage: SequenceExtractor " + "beast_input_file.xml output_file.nexus");
        System.exit(0);
    }
    try {
        XMLParser parser = new XMLParser();
        Runnable runnable = parser.parseFile(new File(args[0]));
        Set<Alignment> alignments = findAlignments(runnable);
        if (alignments.isEmpty()) {
            System.out.println("No alignments found!");
            System.exit(1);
        }
        if (alignments.size() > 1) {
            String prefix;
            int extIndex = args[0].lastIndexOf('.');
            if (extIndex < 0) {
                // No extension
                prefix = args[0];
            } else {
                prefix = args[0].substring(0, extIndex);
            }
            for (Alignment alignment : alignments) {
                if (alignment instanceof FilteredAlignment)
                    continue;
                NexusWriter.write(alignment, null, new PrintStream(prefix + "_" + alignment.getID() + ".nexus"));
            }
        } else {
            NexusWriter.write((Alignment) alignments.toArray()[0], null, new PrintStream(args[1]));
        }
    } catch (FileNotFoundException ex) {
        System.out.println("Could not find file '" + args[0] + "'.");
        System.exit(1);
    } catch (IllegalArgumentException | IllegalAccessException ex) {
        Logger.getLogger(SequenceExtractor.class.getName()).log(Level.SEVERE, null, ex);
    } catch (Exception ex) {
        Logger.getLogger(SequenceExtractor.class.getName()).log(Level.SEVERE, null, ex);
    }
}