Examples with NexusBuilder feast.nexus.NexusBuilder used on opensource projects

Example 1 with NexusBuilder

use of feast.nexus.NexusBuilder in project bacter by tgvaughan.

the class SimulatedACG method initAndValidate.

@Override
public void initAndValidate() {
    rho = rhoInput.get();
    delta = deltaInput.get();
    popFunc = popFuncInput.get();
    // Need to do this here as Tree.processTraits(), which is called
    // by hasDateTrait() and hence simulateClonalFrame(), expects a
    // tree with nodes.
    super.initAndValidate();
    if (clonalFrameInput.get() == null)
        simulateClonalFrame();
    else
        assignFromWithoutID(clonalFrameInput.get());
    // Need to do this here as this sets the tree object that the nodes
    // point to, so without it they point to the dummy tree created by
    // super.initAndValidate().
    initArrays();
    // Generate recombinations
    generateConversions();
    // Write output file
    if (outputFileNameInput.get() != null) {
        NexusBuilder nexusBuilder = new NexusBuilder();
        nexusBuilder.append(new TaxaBlock(m_taxonset.get()));
        nexusBuilder.append((new TreesBlock() {

            @Override
            public String getTreeString(Tree tree) {
                return ((ConversionGraph) tree).getExtendedNewick();
            }
        }).addTree(this, "simulatedARG"));
        nexusBuilder.append(new NexusBlock() {

            @Override
            public String getBlockName() {
                return "bacter";
            }

            @Override
            public List<String> getBlockLines() {
                List<String> lines = new ArrayList<>();
                String lociLine = "loci";
                for (Locus locus : getLoci()) lociLine += " " + locus.getID() + ":" + locus.getSiteCount();
                lines.add(lociLine);
                lines.add("clonalframe_labeled " + root.toNewick());
                lines.add("clonalframe_numbered " + root.toShortNewick(true));
                for (Locus locus : getLoci()) {
                    for (Conversion conv : getConversions(locus)) {
                        lines.add("conversion node1=" + conv.getNode1().getNr() + " node2=" + conv.getNode2().getNr() + " site1=" + conv.getStartSite() + " site2=" + conv.getEndSite() + " locus=" + locus.getID());
                    }
                }
                return lines;
            }
        });
        try (PrintStream pstream = new PrintStream(outputFileNameInput.get())) {
            nexusBuilder.write(pstream);
        } catch (FileNotFoundException e) {
            e.printStackTrace();
        }
    }
}

Example 2 with NexusBuilder

use of feast.nexus.NexusBuilder in project bacter by tgvaughan.

the class SimulatedAlignment method initAndValidate.

@Override
public void initAndValidate() {
    acg = acgInput.get();
    siteModel = siteModelInput.get();
    Locus locus;
    if (acg.getLoci().size() == 1)
        locus = acg.getLoci().get(0);
    else {
        locus = locusInput.get();
        if (locus == null)
            throw new IllegalArgumentException("Must specify locus" + " when simulating alignment from ACG associated" + " with multiple loci.");
    }
    // We can't wait for Alignment.initAndValidate() to get the
    // data type for us.
    grabDataType();
    // Simulate alignment
    simulate(locus);
    super.initAndValidate();
    // Write simulated alignment to disk if requested:
    if (outputFileNameInput.get() != null) {
        try (PrintStream pstream = new PrintStream(outputFileNameInput.get())) {
            if (useNexusInput.get()) {
                NexusBuilder nb = new NexusBuilder();
                nb.append(new TaxaBlock(acg.getTaxonset()));
                nb.append(new CharactersBlock(this));
                nb.write(pstream);
            } else {
                for (String taxonName : acg.getTaxaNames()) {
                    pstream.print(">" + taxonName + "\n");
                    pstream.print(getSequenceAsString(taxonName) + "\n");
                }
            }
        } catch (FileNotFoundException e) {
            e.printStackTrace();
        }
    }
}